diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/property_files/jpt_jpa_core_validation.properties b/jpa/plugins/org.eclipse.jpt.jpa.core/property_files/jpt_jpa_core_validation.properties
index 13f8f62..eda9209 100644
--- a/jpa/plugins/org.eclipse.jpt.jpa.core/property_files/jpt_jpa_core_validation.properties
+++ b/jpa/plugins/org.eclipse.jpt.jpa.core/property_files/jpt_jpa_core_validation.properties
@@ -58,12 +58,13 @@
 ENTITY_NO_PK=The entity has no primary key attribute defined
 ENTITY_NON_ROOT_ID_ATTRIBUTE_SPECIFIED=A primary key attribute should only be defined on the root entity or a mapped superclass
 ENTITY_NON_ROOT_ID_CLASS_SPECIFIED=An ID class should only be defined on the root entity or a mapped superclass
-TYPE_ANNOTATED_BUT_NOT_LISTED_IN_PERSISTENCE_XML=Class \"{0}\" is annotated, but not listed in the persistence.xml file
-TYPE_MANAGED_BUT_NOT_LISTED_IN_PERSISTENCE_XML=Class \"{0}\" is managed, but is not listed in the persistence.xml file
-PERSISTENT_TYPE_DUPLICATE_CLASS=Duplicate class \"{0}\" found in mapping files. This configuration is not supported by the tooling and may result in invalid error messages.
 MANAGED_TYPE_UNRESOLVED_CLASS=Class \"{0}\" cannot be resolved
 MANAGED_TYPE_UNSPECIFIED_CLASS=Unspecified class
+ROOT_ENTITY_HAS_PK_JOIN_COLUMN_DEFINED=Root entity should not have primary key join column defined
+PERSISTENT_TYPE_DUPLICATE_CLASS=Duplicate class \"{0}\" found in mapping files. This configuration is not supported by the tooling and may result in invalid error messages.
 TARGET_NOT_AN_EMBEDDABLE={0} is not mapped as an embeddable
+TYPE_ANNOTATED_BUT_NOT_LISTED_IN_PERSISTENCE_XML=Class \"{0}\" is annotated, but not listed in the persistence.xml file
+TYPE_MANAGED_BUT_NOT_LISTED_IN_PERSISTENCE_XML=Class \"{0}\" is managed, but is not listed in the persistence.xml file
 TYPE_MAPPING_CLASS_MISSING_NO_ARG_CONSTRUCTOR=The Java class for mapped type \"{0}\" must define a non-private zero-argument constructor
 TYPE_MAPPING_CLASS_PRIVATE_NO_ARG_CONSTRUCTOR=The Java class for mapped type \"{0}\" has a private zero-argument constructor; it must be public or protected
 TYPE_MAPPING_FINAL_CLASS=The Java class for mapped type \"{0}\" is final
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/property_files/jpt_jpa_core_validation_description.properties b/jpa/plugins/org.eclipse.jpt.jpa.core/property_files/jpt_jpa_core_validation_description.properties
index 57d8fb4..b7c0b5f 100644
--- a/jpa/plugins/org.eclipse.jpt.jpa.core/property_files/jpt_jpa_core_validation_description.properties
+++ b/jpa/plugins/org.eclipse.jpt.jpa.core/property_files/jpt_jpa_core_validation_description.properties
@@ -53,12 +53,13 @@
 ENTITY_NO_PK=Entity has no primary key
 ENTITY_NON_ROOT_ID_ATTRIBUTE_SPECIFIED=Primary key attribute should only be defined on the root entity or a mapped superclass
 ENTITY_NON_ROOT_ID_CLASS_SPECIFIED=ID class should only be defined on the root entity or a mapped superclass
-TYPE_ANNOTATED_BUT_NOT_LISTED_IN_PERSISTENCE_XML=Class is annotated, but is not listed in the persistence.xml file
-TYPE_MANAGED_BUT_NOT_LISTED_IN_PERSISTENCE_XML=Class is managed, but is not listed in the persistence.xml file
-PERSISTENT_TYPE_DUPLICATE_CLASS=Duplicate ORM class
 MANAGED_TYPE_UNRESOLVED_CLASS=Class in orm.xml cannot be resolved to a java class
 MANAGED_TYPE_UNSPECIFIED_CLASS=Class is unspecified in orm.xml
+PERSISTENT_TYPE_DUPLICATE_CLASS=Duplicate ORM class
+ROOT_ENTITY_HAS_PK_JOIN_COLUMN_DEFINED=Root entity should not have primary key join column defined
 TARGET_NOT_AN_EMBEDDABLE=Target type of an embedded mapping is not an embeddable
+TYPE_ANNOTATED_BUT_NOT_LISTED_IN_PERSISTENCE_XML=Class is annotated, but is not listed in the persistence.xml file
+TYPE_MANAGED_BUT_NOT_LISTED_IN_PERSISTENCE_XML=Class is managed, but is not listed in the persistence.xml file
 TYPE_MAPPING_CLASS_MISSING_NO_ARG_CONSTRUCTOR=Mapped Java class has no no-arg constructor
 TYPE_MAPPING_CLASS_PRIVATE_NO_ARG_CONSTRUCTOR=Mapped Java class has a private no-arg constructor
 TYPE_MAPPING_FINAL_CLASS=Mapped Java class is final
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/context/java/AbstractJavaEntity.java b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/context/java/AbstractJavaEntity.java
index e2e85ff..c7494d5 100644
--- a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/context/java/AbstractJavaEntity.java
+++ b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/context/java/AbstractJavaEntity.java
@@ -80,13 +80,13 @@
 import org.eclipse.jpt.jpa.core.internal.jpa1.context.AttributeOverrideColumnValidator;
 import org.eclipse.jpt.jpa.core.internal.jpa1.context.AttributeOverrideValidator;
 import org.eclipse.jpt.jpa.core.internal.jpa1.context.DiscriminatorColumnValidator;
+import org.eclipse.jpt.jpa.core.internal.jpa1.context.EntityPrimaryKeyJoinColumnValidator;
 import org.eclipse.jpt.jpa.core.internal.jpa1.context.EntityTableDescriptionProvider;
 import org.eclipse.jpt.jpa.core.internal.jpa1.context.GenericEntityPrimaryKeyValidator;
 import org.eclipse.jpt.jpa.core.internal.jpa1.context.JoinTableTableDescriptionProvider;
 import org.eclipse.jpt.jpa.core.internal.jpa1.context.MappedSuperclassOverrideDescriptionProvider;
 import org.eclipse.jpt.jpa.core.internal.jpa1.context.SecondaryTableValidator;
 import org.eclipse.jpt.jpa.core.internal.jpa1.context.TableValidator;
-import org.eclipse.jpt.jpa.core.internal.jpa1.context.java.JavaEntityPrimaryKeyJoinColumnValidator;
 import org.eclipse.jpt.jpa.core.internal.resource.java.NullPrimaryKeyJoinColumnAnnotation;
 import org.eclipse.jpt.jpa.core.jpa2.context.java.JavaAssociationOverrideContainer2_0;
 import org.eclipse.jpt.jpa.core.jpa2.context.java.JavaAttributeOverrideContainer2_0;
@@ -539,16 +539,15 @@
 	}
 
 	public void convertDefaultPrimaryKeyJoinColumnsToSpecified() {
-		if (this.defaultPrimaryKeyJoinColumn == null) {
-			throw new IllegalStateException("default PK join column is null"); //$NON-NLS-1$
-		}
-		// Add a PK join column by creating a specified one using the default one
-		String columnName = this.defaultPrimaryKeyJoinColumn.getDefaultName();
-		String referencedColumnName = this.defaultPrimaryKeyJoinColumn.getDefaultReferencedColumnName();
-
-		SpecifiedPrimaryKeyJoinColumn pkJoinColumn = this.addSpecifiedPrimaryKeyJoinColumn(0);
-		pkJoinColumn.setSpecifiedName(columnName);
-		pkJoinColumn.setSpecifiedReferencedColumnName(referencedColumnName);
+		// This is for root entities which have no default PK join column
+		 SpecifiedPrimaryKeyJoinColumn pkJoinColumn = this.addSpecifiedPrimaryKeyJoinColumn(0);
+		 // Add a PK join column by creating a specified one using the default one
+		 if (this.defaultPrimaryKeyJoinColumn != null) {
+			 String columnName = this.defaultPrimaryKeyJoinColumn.getDefaultName();
+			 String referencedColumnName = this.defaultPrimaryKeyJoinColumn.getDefaultReferencedColumnName();
+			 pkJoinColumn.setSpecifiedName(columnName);
+			 pkJoinColumn.setSpecifiedReferencedColumnName(referencedColumnName);
+		 }
 	}
 
 	public void clearSpecifiedPrimaryKeyJoinColumns() {
@@ -648,7 +647,7 @@
 	}
 
 	protected boolean buildsDefaultPrimaryKeyJoinColumn() {
-		return ! this.hasSpecifiedPrimaryKeyJoinColumns();
+		return ! this.isRootEntity() && ! this.hasSpecifiedPrimaryKeyJoinColumns();
 	}
 
 	protected JavaSpecifiedPrimaryKeyJoinColumn buildDefaultPrimaryKeyJoinColumn() {
@@ -1252,9 +1251,7 @@
 			secondaryTable.validate(messages, reporter);
 		}
 		this.validateInheritance(messages, reporter);
-		for (JavaSpecifiedPrimaryKeyJoinColumn pkJoinColumn : this.getPrimaryKeyJoinColumns()) {
-			pkJoinColumn.validate(messages, reporter);
-		}
+		this.validatePrimaryKeyJoinColumns(messages, reporter);
 		this.generatorContainer.validate(messages, reporter);
 		this.queryContainer.validate(messages, reporter);
 		this.attributeOverrideContainer.validate(messages, reporter);
@@ -1263,6 +1260,24 @@
 		this.idClassReference.validate(messages, reporter);
 	}
 
+	protected void validatePrimaryKeyJoinColumns(List<IMessage> messages, IReporter reporter) {
+		if (this.getPrimaryKeyJoinColumnsSize() > 0) {
+			if (this.getParentEntity() == null) {
+				messages.add(
+						this.buildValidationMessage(
+								this.getMappingAnnotation().getNameTextRange(),
+								JptJpaCoreValidationMessages.ROOT_ENTITY_HAS_PK_JOIN_COLUMN_DEFINED,
+								this.getPersistentType().getName()
+						)
+				);
+			} else {
+				for (JavaSpecifiedPrimaryKeyJoinColumn pkJoinColumn : this.getPrimaryKeyJoinColumns()) {
+					pkJoinColumn.validate(messages, reporter);
+				}
+			}
+		}
+	}
+
 	@Override
 	public boolean validatesAgainstDatabase() {
 		return super.validatesAgainstDatabase() && ! this.isAbstractTablePerClass();
@@ -1619,7 +1634,7 @@
 		}
 
 		public JpaValidator buildColumnValidator(NamedColumn column) {
-			return new JavaEntityPrimaryKeyJoinColumnValidator((BaseJoinColumn) column, this, AbstractJavaEntity.this);
+			return new EntityPrimaryKeyJoinColumnValidator((BaseJoinColumn) column, this);
 		}
 	}
 
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/context/orm/AbstractOrmEntity.java b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/context/orm/AbstractOrmEntity.java
index 78b146a..a1ae765 100644
--- a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/context/orm/AbstractOrmEntity.java
+++ b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/context/orm/AbstractOrmEntity.java
@@ -799,6 +799,11 @@
 	}
 
 	public void convertDefaultPrimaryKeyJoinColumnsToSpecified() {
+		// This is necessary for root entities which have no default PK join column
+		if (this.getPrimaryKeyJoinColumnsSize() == 0) {
+			this.addSpecifiedPrimaryKeyJoinColumn();
+		}
+		
 		for (PrimaryKeyJoinColumn defaultJoinColumn : this.getDefaultPrimaryKeyJoinColumns()) {
 			String columnName = defaultJoinColumn.getName();
 			String referencedColumnName = defaultJoinColumn.getReferencedColumnName();
@@ -903,7 +908,7 @@
 				if (this.javaPrimaryKeyJoinColumnsWillBeDefaults()) {
 					// specified => java
 					this.initializeVirtualPrimaryKeyJoinColumns();
-				} else {
+				} else if (this.getParentEntity() != null) {
 					// specified => default
 					this.addDefaultPrimaryKeyJoinColumn();
 				}
@@ -1710,9 +1715,7 @@
 			secondaryTable.validate(messages, reporter);
 		}
 		this.validateInheritance(messages, reporter);
-		for (OrmSpecifiedPrimaryKeyJoinColumn pkJoinColumn : this.getSpecifiedPrimaryKeyJoinColumns()) {
-			pkJoinColumn.validate(messages, reporter);
-		}
+		this.validatePrimaryKeyJoinColumns(messages, reporter);
 		this.attributeOverrideContainer.validate(messages, reporter);
 		this.associationOverrideContainer.validate(messages, reporter);
 		this.generatorContainer.validate(messages, reporter);
@@ -1721,6 +1724,25 @@
 		this.idClassReference.validate(messages, reporter);
 	}
 
+	protected void validatePrimaryKeyJoinColumns(List<IMessage> messages, IReporter reporter) {
+		if (this.getPrimaryKeyJoinColumnsSize() > 0) {
+			if (this.getParentEntity() == null) {
+				messages.add(
+						this.buildValidationMessage(
+								this.getNameTextRange(),
+								JptJpaCoreValidationMessages.ROOT_ENTITY_HAS_PK_JOIN_COLUMN_DEFINED,
+								this.getPersistentType().getName()
+						)
+				);
+			} else {
+				for (OrmSpecifiedPrimaryKeyJoinColumn pkJoinColumn : this.getSpecifiedPrimaryKeyJoinColumns()) {
+					pkJoinColumn.validate(messages, reporter);
+				}
+			}
+		}
+		
+	}
+
 	protected void validateEntityName(List<IMessage> messages) {
 		if (StringTools.isBlank(this.getName())){
 			messages.add(
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/jpa1/context/java/JavaEntityPrimaryKeyJoinColumnValidator.java b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/jpa1/context/java/JavaEntityPrimaryKeyJoinColumnValidator.java
deleted file mode 100644
index c2e3236..0000000
--- a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/jpa1/context/java/JavaEntityPrimaryKeyJoinColumnValidator.java
+++ /dev/null
@@ -1,40 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2013 Oracle. All rights reserved.
- * This program and the accompanying materials are made available under the
- * terms of the Eclipse Public License v1.0, which accompanies this distribution
- * and is available at http://www.eclipse.org/legal/epl-v10.html.
- * 
- * Contributors:
- *     Oracle - initial API and implementation
- ******************************************************************************/
-package org.eclipse.jpt.jpa.core.internal.jpa1.context.java;
-
-import java.util.List;
-import org.eclipse.jpt.jpa.core.context.BaseJoinColumn;
-import org.eclipse.jpt.jpa.core.internal.context.java.AbstractJavaEntity;
-import org.eclipse.jpt.jpa.core.internal.jpa1.context.EntityPrimaryKeyJoinColumnValidator;
-import org.eclipse.wst.validation.internal.provisional.core.IMessage;
-
-public class JavaEntityPrimaryKeyJoinColumnValidator
-	extends EntityPrimaryKeyJoinColumnValidator
-{
-	protected final AbstractJavaEntity entity;
-
-	public JavaEntityPrimaryKeyJoinColumnValidator(
-			BaseJoinColumn column,
-			BaseJoinColumn.ParentAdapter parentAdapter,
-			AbstractJavaEntity entity) {
-		super(column, parentAdapter);
-		this.entity = entity;
-	}
-
-	@Override
-	protected void validateJoinColumnName(List<IMessage> messages) {
-		// Based on the spec., the PrimaryKeyJoinColumn annotation is really only meaningful when 
-		// applying on an entity subclass so we only validate it when an entity is a descendant or an entity
-		// has specified primary key join columns
-		if (this.entity.isDescendant() || this.entity.getSpecifiedPrimaryKeyJoinColumnsSize() > 0) {
-			super.validateJoinColumnName(messages);
-		}
-	}
-}
\ No newline at end of file
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/validation/JptJpaCoreValidationMessages.java b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/validation/JptJpaCoreValidationMessages.java
index e64f4de..7272c06 100644
--- a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/validation/JptJpaCoreValidationMessages.java
+++ b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/validation/JptJpaCoreValidationMessages.java
@@ -72,6 +72,7 @@
 	public static ValidationMessage TYPE_MANAGED_BUT_NOT_LISTED_IN_PERSISTENCE_XML;
 	public static ValidationMessage MANAGED_TYPE_UNRESOLVED_CLASS;
 	public static ValidationMessage MANAGED_TYPE_UNSPECIFIED_CLASS;
+	public static ValidationMessage ROOT_ENTITY_HAS_PK_JOIN_COLUMN_DEFINED;
 	public static ValidationMessage TARGET_NOT_AN_EMBEDDABLE;
 	public static ValidationMessage TYPE_MAPPING_CLASS_MISSING_NO_ARG_CONSTRUCTOR;
 	public static ValidationMessage TYPE_MAPPING_CLASS_PRIVATE_NO_ARG_CONSTRUCTOR;
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.ui/src/org/eclipse/jpt/jpa/ui/internal/prefs/JpaProblemSeveritiesPage.java b/jpa/plugins/org.eclipse.jpt.jpa.ui/src/org/eclipse/jpt/jpa/ui/internal/prefs/JpaProblemSeveritiesPage.java
index 3379774..70dbc2b 100644
--- a/jpa/plugins/org.eclipse.jpt.jpa.ui/src/org/eclipse/jpt/jpa/ui/internal/prefs/JpaProblemSeveritiesPage.java
+++ b/jpa/plugins/org.eclipse.jpt.jpa.ui/src/org/eclipse/jpt/jpa/ui/internal/prefs/JpaProblemSeveritiesPage.java
@@ -117,10 +117,11 @@
 		this.addLabeledCombo(parent, JptJpaCoreValidationMessages.ENTITY_NO_PK);
 		this.addLabeledCombo(parent, JptJpaCoreValidationMessages.ENTITY_NON_ROOT_ID_ATTRIBUTE_SPECIFIED); //3.0 M7
 		this.addLabeledCombo(parent, JptJpaCoreValidationMessages.ENTITY_NON_ROOT_ID_CLASS_SPECIFIED); //3.0 M7
-		this.addLabeledCombo(parent, JptJpaCoreValidationMessages.TYPE_ANNOTATED_BUT_NOT_LISTED_IN_PERSISTENCE_XML);
-		this.addLabeledCombo(parent, JptJpaCoreValidationMessages.TYPE_MANAGED_BUT_NOT_LISTED_IN_PERSISTENCE_XML);
 		this.addLabeledCombo(parent, JptJpaCoreValidationMessages.MANAGED_TYPE_UNRESOLVED_CLASS);
 		this.addLabeledCombo(parent, JptJpaCoreValidationMessages.MANAGED_TYPE_UNSPECIFIED_CLASS);
+		this.addLabeledCombo(parent, JptJpaCoreValidationMessages.ROOT_ENTITY_HAS_PK_JOIN_COLUMN_DEFINED);
+		this.addLabeledCombo(parent, JptJpaCoreValidationMessages.TYPE_ANNOTATED_BUT_NOT_LISTED_IN_PERSISTENCE_XML);
+		this.addLabeledCombo(parent, JptJpaCoreValidationMessages.TYPE_MANAGED_BUT_NOT_LISTED_IN_PERSISTENCE_XML);
 		this.addLabeledCombo(parent, JptJpaCoreValidationMessages.TYPE_MAPPING_CLASS_MISSING_NO_ARG_CONSTRUCTOR);
 		this.addLabeledCombo(parent, JptJpaCoreValidationMessages.TYPE_MAPPING_CLASS_PRIVATE_NO_ARG_CONSTRUCTOR);
 		this.addLabeledCombo(parent, JptJpaCoreValidationMessages.TYPE_MAPPING_FINAL_CLASS);
diff --git a/jpa/tests/org.eclipse.jpt.jpa.core.tests/src/org/eclipse/jpt/jpa/core/tests/internal/context/java/JavaEntityTests.java b/jpa/tests/org.eclipse.jpt.jpa.core.tests/src/org/eclipse/jpt/jpa/core/tests/internal/context/java/JavaEntityTests.java
index 5749a5f..7c4e60e 100644
--- a/jpa/tests/org.eclipse.jpt.jpa.core.tests/src/org/eclipse/jpt/jpa/core/tests/internal/context/java/JavaEntityTests.java
+++ b/jpa/tests/org.eclipse.jpt.jpa.core.tests/src/org/eclipse/jpt/jpa/core/tests/internal/context/java/JavaEntityTests.java
@@ -20,9 +20,7 @@
 import org.eclipse.jpt.common.utility.internal.iterator.IteratorTools;
 import org.eclipse.jpt.jpa.core.MappingKeys;
 import org.eclipse.jpt.jpa.core.context.AccessType;
-import org.eclipse.jpt.jpa.core.context.SpecifiedAssociationOverride;
 import org.eclipse.jpt.jpa.core.context.AssociationOverrideContainer;
-import org.eclipse.jpt.jpa.core.context.SpecifiedAttributeOverride;
 import org.eclipse.jpt.jpa.core.context.AttributeOverrideContainer;
 import org.eclipse.jpt.jpa.core.context.BasicMapping;
 import org.eclipse.jpt.jpa.core.context.DiscriminatorType;
@@ -30,30 +28,32 @@
 import org.eclipse.jpt.jpa.core.context.Entity;
 import org.eclipse.jpt.jpa.core.context.IdMapping;
 import org.eclipse.jpt.jpa.core.context.InheritanceType;
-import org.eclipse.jpt.jpa.core.context.SpecifiedJoinColumn;
+import org.eclipse.jpt.jpa.core.context.JoinColumn;
+import org.eclipse.jpt.jpa.core.context.JoinColumnRelationship;
+import org.eclipse.jpt.jpa.core.context.JoinColumnRelationshipStrategy;
 import org.eclipse.jpt.jpa.core.context.MappedSuperclass;
 import org.eclipse.jpt.jpa.core.context.NamedNativeQuery;
 import org.eclipse.jpt.jpa.core.context.NamedQuery;
 import org.eclipse.jpt.jpa.core.context.OneToOneMapping;
 import org.eclipse.jpt.jpa.core.context.PersistentType;
+import org.eclipse.jpt.jpa.core.context.SpecifiedAssociationOverride;
+import org.eclipse.jpt.jpa.core.context.SpecifiedAttributeOverride;
+import org.eclipse.jpt.jpa.core.context.SpecifiedJoinColumn;
 import org.eclipse.jpt.jpa.core.context.SpecifiedPrimaryKeyJoinColumn;
-import org.eclipse.jpt.jpa.core.context.JoinColumn;
-import org.eclipse.jpt.jpa.core.context.JoinColumnRelationship;
-import org.eclipse.jpt.jpa.core.context.JoinColumnRelationshipStrategy;
-import org.eclipse.jpt.jpa.core.context.Table;
 import org.eclipse.jpt.jpa.core.context.SpecifiedSecondaryTable;
 import org.eclipse.jpt.jpa.core.context.SpecifiedTable;
+import org.eclipse.jpt.jpa.core.context.Table;
 import org.eclipse.jpt.jpa.core.context.VirtualAssociationOverride;
 import org.eclipse.jpt.jpa.core.context.VirtualAttributeOverride;
-import org.eclipse.jpt.jpa.core.context.java.JavaSpecifiedAssociationOverride;
 import org.eclipse.jpt.jpa.core.context.java.JavaAssociationOverrideContainer;
-import org.eclipse.jpt.jpa.core.context.java.JavaSpecifiedAttributeOverride;
 import org.eclipse.jpt.jpa.core.context.java.JavaAttributeOverrideContainer;
 import org.eclipse.jpt.jpa.core.context.java.JavaEntity;
 import org.eclipse.jpt.jpa.core.context.java.JavaIdMapping;
 import org.eclipse.jpt.jpa.core.context.java.JavaNamedNativeQuery;
 import org.eclipse.jpt.jpa.core.context.java.JavaNamedQuery;
 import org.eclipse.jpt.jpa.core.context.java.JavaPersistentType;
+import org.eclipse.jpt.jpa.core.context.java.JavaSpecifiedAssociationOverride;
+import org.eclipse.jpt.jpa.core.context.java.JavaSpecifiedAttributeOverride;
 import org.eclipse.jpt.jpa.core.context.java.JavaSpecifiedPrimaryKeyJoinColumn;
 import org.eclipse.jpt.jpa.core.context.java.JavaSpecifiedSecondaryTable;
 import org.eclipse.jpt.jpa.core.context.java.JavaVirtualAssociationOverride;
@@ -1453,7 +1453,9 @@
 	}
 
 	public void testPrimaryKeyJoinColumnsSize() throws Exception {
-		createTestEntityWithSecondaryTable();
+		createTestEntity();
+		createTestSubType();
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
 		
 		//just the default pkJoinColumn, so 1
@@ -1468,7 +1470,9 @@
 	}
 
 	public void testGetDefaultPrimaryKeyJoinColumn() throws Exception {
-		createTestEntityWithSecondaryTable();
+		createTestEntity();
+		createTestSubType();
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
 		
 		assertNotNull(getJavaEntity().getDefaultPrimaryKeyJoinColumn());
@@ -1650,7 +1654,9 @@
 	}
 	
 	public void testPrimaryKeyJoinColumnIsVirtual() throws Exception {
-		createTestEntityWithSecondaryTable();
+		createTestEntity();
+		createTestSubType();
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
 		
 		assertTrue(getJavaEntity().getDefaultPrimaryKeyJoinColumn().isVirtual());
diff --git a/jpa/tests/org.eclipse.jpt.jpa.core.tests/src/org/eclipse/jpt/jpa/core/tests/internal/context/java/JavaPrimaryKeyJoinColumnTests.java b/jpa/tests/org.eclipse.jpt.jpa.core.tests/src/org/eclipse/jpt/jpa/core/tests/internal/context/java/JavaPrimaryKeyJoinColumnTests.java
index 1450205..dc6bc04 100644
--- a/jpa/tests/org.eclipse.jpt.jpa.core.tests/src/org/eclipse/jpt/jpa/core/tests/internal/context/java/JavaPrimaryKeyJoinColumnTests.java
+++ b/jpa/tests/org.eclipse.jpt.jpa.core.tests/src/org/eclipse/jpt/jpa/core/tests/internal/context/java/JavaPrimaryKeyJoinColumnTests.java
@@ -11,8 +11,8 @@
 
 import java.util.Iterator;
 import org.eclipse.jdt.core.ICompilationUnit;
-import org.eclipse.jpt.common.core.resource.java.JavaResourceType;
 import org.eclipse.jpt.common.core.resource.java.JavaResourceAnnotatedElement.AstNodeType;
+import org.eclipse.jpt.common.core.resource.java.JavaResourceType;
 import org.eclipse.jpt.common.utility.internal.ObjectTools;
 import org.eclipse.jpt.common.utility.internal.iterator.IteratorTools;
 import org.eclipse.jpt.jpa.core.MappingKeys;
@@ -47,13 +47,39 @@
 		});
 	}
 
+	private ICompilationUnit createTestSubEntity() throws Exception {
+		return this.createTestType(PACKAGE_NAME, "AnnotationTestTypeChild.java", "AnnotationTestTypeChild", new DefaultAnnotationWriter() {
+			@Override
+			public Iterator<String> imports() {
+				return IteratorTools.iterator(JPA.ENTITY, JPA.ID);
+			}
+			@Override
+			public void appendExtendsImplementsTo(StringBuilder sb) {
+				sb.append("extends " + TYPE_NAME + " ");
+			}
+			@Override
+			public void appendTypeAnnotationTo(StringBuilder sb) {
+				sb.append("@Entity");
+			}
+
+			@Override
+			public void appendIdFieldAnnotationTo(StringBuilder sb) {
+				sb.append("@Id");
+			}
+		});
+	}
+
 	private ICompilationUnit createTestEntityWithPrimaryKeyJoinColumn() throws Exception {	
-		return this.createTestType(new DefaultAnnotationWriter() {
+		return this.createTestType(PACKAGE_NAME, "AnnotationTestTypeChild.java", "AnnotationTestTypeChild", new DefaultAnnotationWriter() {
 			@Override
 			public Iterator<String> imports() {
 				return IteratorTools.iterator(JPA.ENTITY, JPA.ID, JPA.PRIMARY_KEY_JOIN_COLUMN);
 			}
 			@Override
+			public void appendExtendsImplementsTo(StringBuilder sb) {
+				sb.append("extends " + TYPE_NAME + " ");
+			}
+			@Override
 			public void appendTypeAnnotationTo(StringBuilder sb) {
 				sb.append("@Entity").append(CR);
 				sb.append("@PrimaryKeyJoinColumn(name=\"" + PRIMARY_KEY_JOIN_COLUMN_NAME + "\")");
@@ -72,13 +98,13 @@
 	
 	public void testGetSpecifiedName() throws Exception {
 		createTestEntityWithPrimaryKeyJoinColumn();
-		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 
 		SpecifiedPrimaryKeyJoinColumn specifiedPkJoinColumn = getJavaEntity().getSpecifiedPrimaryKeyJoinColumns().iterator().next();
 		assertEquals(PRIMARY_KEY_JOIN_COLUMN_NAME, specifiedPkJoinColumn.getSpecifiedName());
 		
 		
-		JavaResourceType resourceType = (JavaResourceType) getJpaProject().getJavaResourceType(FULLY_QUALIFIED_TYPE_NAME, AstNodeType.TYPE);
+		JavaResourceType resourceType = (JavaResourceType) getJpaProject().getJavaResourceType(PACKAGE_NAME + ".AnnotationTestTypeChild", AstNodeType.TYPE);
 		PrimaryKeyJoinColumnAnnotation pkJoinColumnResource = (PrimaryKeyJoinColumnAnnotation) resourceType.getAnnotation(0, JPA.PRIMARY_KEY_JOIN_COLUMN);
 		
 		pkJoinColumnResource.setName("FOO");
@@ -89,6 +115,8 @@
 	
 	public void testGetDefaultNameNoSpecifiedPrimaryKeyJoinColumns() throws Exception {
 		createTestEntity();
+		createTestSubEntity();
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
 		
 		SpecifiedPrimaryKeyJoinColumn pkJoinColumn = getJavaEntity().getDefaultPrimaryKeyJoinColumn();
@@ -97,7 +125,7 @@
 
 	public void testGetDefaultName() throws Exception {
 		createTestEntityWithPrimaryKeyJoinColumn();
-		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 		
 		assertNull(getJavaEntity().getDefaultPrimaryKeyJoinColumn());
 		
@@ -113,7 +141,7 @@
 	
 	public void testGetName() throws Exception {
 		createTestEntityWithPrimaryKeyJoinColumn();
-		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 		
 		SpecifiedPrimaryKeyJoinColumn specifiedPkJoinColumn = getJavaEntity().getSpecifiedPrimaryKeyJoinColumns().iterator().next();
 		assertEquals(PRIMARY_KEY_JOIN_COLUMN_NAME, specifiedPkJoinColumn.getName());
@@ -121,14 +149,14 @@
 
 	public void testSetSpecifiedName() throws Exception {
 		createTestEntityWithPrimaryKeyJoinColumn();
-		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 
 		SpecifiedPrimaryKeyJoinColumn specifiedPkJoinColumn = getJavaEntity().getSpecifiedPrimaryKeyJoinColumns().iterator().next();
 		
 		specifiedPkJoinColumn.setSpecifiedName("foo");
 		assertEquals("foo", specifiedPkJoinColumn.getSpecifiedName());
 		
-		JavaResourceType resourceType = (JavaResourceType) getJpaProject().getJavaResourceType(FULLY_QUALIFIED_TYPE_NAME, AstNodeType.TYPE);
+		JavaResourceType resourceType = (JavaResourceType) getJpaProject().getJavaResourceType(PACKAGE_NAME + ".AnnotationTestTypeChild", AstNodeType.TYPE);
 		PrimaryKeyJoinColumnAnnotation columnAnnotation = (PrimaryKeyJoinColumnAnnotation) resourceType.getAnnotation(0, JPA.PRIMARY_KEY_JOIN_COLUMN);
 		
 		assertEquals("foo", columnAnnotation.getName());
@@ -141,12 +169,12 @@
 
 	public void testGetColumnDefinition() throws Exception {
 		createTestEntityWithPrimaryKeyJoinColumn();
-		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
-		
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
+	
 		SpecifiedPrimaryKeyJoinColumn specifiedPkJoinColumn = getJavaEntity().getSpecifiedPrimaryKeyJoinColumns().iterator().next();
 		assertNull(specifiedPkJoinColumn.getColumnDefinition());
 
-		JavaResourceType resourceType = (JavaResourceType) getJpaProject().getJavaResourceType(FULLY_QUALIFIED_TYPE_NAME, AstNodeType.TYPE);
+		JavaResourceType resourceType = (JavaResourceType) getJpaProject().getJavaResourceType(PACKAGE_NAME + ".AnnotationTestTypeChild", AstNodeType.TYPE);
 		PrimaryKeyJoinColumnAnnotation column = (PrimaryKeyJoinColumnAnnotation) resourceType.getAnnotation(0, JPA.PRIMARY_KEY_JOIN_COLUMN);
 		column.setColumnDefinition(COLUMN_DEFINITION);
 		getJpaProject().synchronizeContextModel();
@@ -166,12 +194,12 @@
 	
 	public void testSetColumnDefinition() throws Exception {
 		createTestEntityWithPrimaryKeyJoinColumn();
-		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 		
 		SpecifiedPrimaryKeyJoinColumn specifiedPkJoinColumn = getJavaEntity().getSpecifiedPrimaryKeyJoinColumns().iterator().next();
 		specifiedPkJoinColumn.setColumnDefinition("foo");
 		
-		JavaResourceType resourceType = (JavaResourceType) getJpaProject().getJavaResourceType(FULLY_QUALIFIED_TYPE_NAME, AstNodeType.TYPE);
+		JavaResourceType resourceType = (JavaResourceType) getJpaProject().getJavaResourceType(PACKAGE_NAME + ".AnnotationTestTypeChild", AstNodeType.TYPE);
 		PrimaryKeyJoinColumnAnnotation column = (PrimaryKeyJoinColumnAnnotation) resourceType.getAnnotation(0, JPA.PRIMARY_KEY_JOIN_COLUMN);
 		
 		assertEquals("foo", column.getColumnDefinition());
@@ -183,12 +211,12 @@
 
 	public void testGetSpecifiedReferencedColumnName() throws Exception {
 		createTestEntityWithPrimaryKeyJoinColumn();
-		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 
 		SpecifiedPrimaryKeyJoinColumn specifiedPkJoinColumn = getJavaEntity().getSpecifiedPrimaryKeyJoinColumns().iterator().next();
 		assertNull(specifiedPkJoinColumn.getSpecifiedReferencedColumnName());
 		
-		JavaResourceType resourceType = (JavaResourceType) getJpaProject().getJavaResourceType(FULLY_QUALIFIED_TYPE_NAME, AstNodeType.TYPE);
+		JavaResourceType resourceType = (JavaResourceType) getJpaProject().getJavaResourceType(PACKAGE_NAME + ".AnnotationTestTypeChild", AstNodeType.TYPE);
 		PrimaryKeyJoinColumnAnnotation pkJoinColumnResource = (PrimaryKeyJoinColumnAnnotation) resourceType.getAnnotation(0, JPA.PRIMARY_KEY_JOIN_COLUMN);
 		
 		pkJoinColumnResource.setReferencedColumnName("FOO");
@@ -199,15 +227,17 @@
 	
 	public void testGetDefaultReferencedColumnNameNoSpecifiedPrimaryKeyJoinColumns() throws Exception {
 		createTestEntity();
+		createTestSubEntity();
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
-		
+
 		SpecifiedPrimaryKeyJoinColumn pkJoinColumn = getJavaEntity().getDefaultPrimaryKeyJoinColumn();
 		assertEquals("id", pkJoinColumn.getDefaultReferencedColumnName());
 	}
 	
 	public void testGetDefaultReferencedColumnName() throws Exception {
 		createTestEntityWithPrimaryKeyJoinColumn();
-		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 		
 		assertNull(getJavaEntity().getDefaultPrimaryKeyJoinColumn());
 		
@@ -224,9 +254,9 @@
 	
 	public void testGetReferencedColumnName() throws Exception {
 		createTestEntityWithPrimaryKeyJoinColumn();
-		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 		
-		JavaResourceType resourceType = (JavaResourceType) getJpaProject().getJavaResourceType(FULLY_QUALIFIED_TYPE_NAME, AstNodeType.TYPE);
+		JavaResourceType resourceType = (JavaResourceType) getJpaProject().getJavaResourceType(PACKAGE_NAME + ".AnnotationTestTypeChild", AstNodeType.TYPE);
 		PrimaryKeyJoinColumnAnnotation pkJoinColumnResource = (PrimaryKeyJoinColumnAnnotation) resourceType.getAnnotation(0, JPA.PRIMARY_KEY_JOIN_COLUMN);
 		
 		pkJoinColumnResource.setReferencedColumnName("FOO");
@@ -238,14 +268,14 @@
 
 	public void testSetSpecifiedReferencedColumnName() throws Exception {
 		createTestEntityWithPrimaryKeyJoinColumn();
-		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 
 		SpecifiedPrimaryKeyJoinColumn specifiedPkJoinColumn = getJavaEntity().getSpecifiedPrimaryKeyJoinColumns().iterator().next();
 		
 		specifiedPkJoinColumn.setSpecifiedReferencedColumnName("foo");
 		assertEquals("foo", specifiedPkJoinColumn.getSpecifiedReferencedColumnName());
 		
-		JavaResourceType resourceType = (JavaResourceType) getJpaProject().getJavaResourceType(FULLY_QUALIFIED_TYPE_NAME, AstNodeType.TYPE);
+		JavaResourceType resourceType = (JavaResourceType) getJpaProject().getJavaResourceType(PACKAGE_NAME + ".AnnotationTestTypeChild", AstNodeType.TYPE);
 		PrimaryKeyJoinColumnAnnotation columnAnnotation = (PrimaryKeyJoinColumnAnnotation) resourceType.getAnnotation(0, JPA.PRIMARY_KEY_JOIN_COLUMN);
 		
 		assertEquals("foo", columnAnnotation.getReferencedColumnName());
@@ -258,9 +288,11 @@
 	}
 	
 	public void testIsVirtual() throws Exception {
+		createTestEntity();
 		createTestEntityWithPrimaryKeyJoinColumn();
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
-
+		
 		SpecifiedPrimaryKeyJoinColumn specifiedPkJoinColumn = getJavaEntity().getSpecifiedPrimaryKeyJoinColumns().iterator().next();
 		assertFalse(specifiedPkJoinColumn.isVirtual());
 		
@@ -271,7 +303,7 @@
 	
 	public void testIsReferencedColumnResolved() throws Exception {
 		createTestEntityWithPrimaryKeyJoinColumn();
-		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 
 		SpecifiedPrimaryKeyJoinColumn specifiedPkJoinColumn = getJavaEntity().getSpecifiedPrimaryKeyJoinColumns().iterator().next();
 		assertFalse(((Boolean) ObjectTools.execute(specifiedPkJoinColumn, "referencedColumnIsResolved")).booleanValue());
@@ -279,7 +311,7 @@
 	
 	public void testDbColumn() throws Exception {
 		createTestEntityWithPrimaryKeyJoinColumn();
-		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 
 		SpecifiedPrimaryKeyJoinColumn specifiedPkJoinColumn = getJavaEntity().getSpecifiedPrimaryKeyJoinColumns().iterator().next();
 		assertFalse(specifiedPkJoinColumn.isResolved());
@@ -287,7 +319,7 @@
 	
 	public void testDbReferencedColumn() throws Exception {
 		createTestEntityWithPrimaryKeyJoinColumn();
-		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 
 		SpecifiedPrimaryKeyJoinColumn specifiedPkJoinColumn = getJavaEntity().getSpecifiedPrimaryKeyJoinColumns().iterator().next();
 		assertFalse(((Boolean) ObjectTools.execute(specifiedPkJoinColumn, "referencedColumnIsResolved")).booleanValue());
@@ -295,7 +327,7 @@
 	
 	public void testDbTable() throws Exception {
 		createTestEntityWithPrimaryKeyJoinColumn();
-		addXmlClassRef(FULLY_QUALIFIED_TYPE_NAME);
+		addXmlClassRef(PACKAGE_NAME + ".AnnotationTestTypeChild");
 
 		SpecifiedPrimaryKeyJoinColumn specifiedPkJoinColumn = getJavaEntity().getSpecifiedPrimaryKeyJoinColumns().iterator().next();
 		assertNull(specifiedPkJoinColumn.getDbTable());