diff --git a/hibernate-core/src/main/java/org/hibernate/HibernateException.java b/hibernate-core/src/main/java/org/hibernate/HibernateException.java
index 5d8895de7c10..7d3d1a8e10b7 100644
--- a/hibernate-core/src/main/java/org/hibernate/HibernateException.java
+++ b/hibernate-core/src/main/java/org/hibernate/HibernateException.java
@@ -6,17 +6,17 @@
  */
 package org.hibernate;
 
+import javax.persistence.PersistenceException;
+
 /**
  * The base exception type for Hibernate exceptions.
  * <p/>
  * Note that all {@link java.sql.SQLException SQLExceptions} will be wrapped in some form of 
  * {@link JDBCException}.
  * 
- * @see JDBCException
- * 
  * @author Gavin King
  */
-public class HibernateException extends RuntimeException {
+public class HibernateException extends PersistenceException {
 	/**
 	 * Constructs a HibernateException using the given exception message.
 	 *
diff --git a/hibernate-core/src/main/java/org/hibernate/internal/SessionImpl.java b/hibernate-core/src/main/java/org/hibernate/internal/SessionImpl.java
index 6acefeb0688f..8320e48ab8e2 100644
--- a/hibernate-core/src/main/java/org/hibernate/internal/SessionImpl.java
+++ b/hibernate-core/src/main/java/org/hibernate/internal/SessionImpl.java
@@ -1240,6 +1240,11 @@ private void fireRefresh(RefreshEvent event) {
 			}
 		}
 		catch (RuntimeException e) {
+			if ( !getSessionFactory().getSessionFactoryOptions().isJpaBootstrap() ) {
+				if ( e instanceof HibernateException ) {
+					throw e;
+				}
+			}
 			//including HibernateException
 			throw convert( e );
 		}
@@ -1258,6 +1263,12 @@ private void fireRefresh(Map refreshedAlready, RefreshEvent event) {
 			delayedAfterCompletion();
 		}
 		catch (RuntimeException e) {
+			if ( !getSessionFactory().getSessionFactoryOptions().isJpaBootstrap() ) {
+				if ( e instanceof HibernateException ) {
+					handlePersistenceException( (HibernateException) e );
+					throw e;
+				}
+			}
 			//including HibernateException
 			throw convert( e );
 		}
diff --git a/hibernate-core/src/test/java/org/hibernate/test/hql/CriteriaHQLAlignmentTest.java b/hibernate-core/src/test/java/org/hibernate/test/hql/CriteriaHQLAlignmentTest.java
index 1053b121503d..de44da752492 100644
--- a/hibernate-core/src/test/java/org/hibernate/test/hql/CriteriaHQLAlignmentTest.java
+++ b/hibernate-core/src/test/java/org/hibernate/test/hql/CriteriaHQLAlignmentTest.java
@@ -325,21 +325,21 @@ public void testCountReturnValues() {
 			}
 			assertEquals( 1, count.longValue() );
 		}
-		catch (PersistenceException e) {
-			SQLGrammarException cause = assertTyping( SQLGrammarException.class, e.getCause() );
+		catch ( SQLGrammarException ex ) {
 			if ( ! getDialect().supportsTupleCounts() ) {
 				// expected
 			}
 			else {
-				throw e;
+				throw ex;
 			}
 		}
-		catch ( SQLGrammarException ex ) {
+		catch (PersistenceException e) {
+			SQLGrammarException cause = assertTyping( SQLGrammarException.class, e.getCause() );
 			if ( ! getDialect().supportsTupleCounts() ) {
 				// expected
 			}
 			else {
-				throw ex;
+				throw e;
 			}
 		}
 		finally {
diff --git a/hibernate-core/src/test/java/org/hibernate/test/tm/TransactionTimeoutTest.java b/hibernate-core/src/test/java/org/hibernate/test/tm/TransactionTimeoutTest.java
index 4d134c790113..102535559479 100644
--- a/hibernate-core/src/test/java/org/hibernate/test/tm/TransactionTimeoutTest.java
+++ b/hibernate-core/src/test/java/org/hibernate/test/tm/TransactionTimeoutTest.java
@@ -70,12 +70,12 @@ public void testTransactionTimeoutFailure() throws InterruptedException {
 			session.persist( new Person( "Lukasz", "Antoniak" ) );
 			transaction.commit();
 		}
-		catch (PersistenceException e) {
-			assertTyping( TransactionException.class, e.getCause() );
-		}
 		catch (TransactionException e) {
 			// expected
 		}
+		catch (PersistenceException e) {
+			assertTyping( TransactionException.class, e.getCause() );
+		}
 		finally {
 			session.close();
 		}
diff --git a/hibernate-entitymanager/src/test/java/org/hibernate/jpa/test/jee/OrmVersionTest.java b/hibernate-entitymanager/src/test/java/org/hibernate/jpa/test/jee/OrmVersionTest.java
index 8b4f51409bb3..7ea59491b289 100644
--- a/hibernate-entitymanager/src/test/java/org/hibernate/jpa/test/jee/OrmVersionTest.java
+++ b/hibernate-entitymanager/src/test/java/org/hibernate/jpa/test/jee/OrmVersionTest.java
@@ -60,15 +60,12 @@ public void testInvalidOrm1() {
 			hp.createContainerEntityManagerFactory( pui, Collections.EMPTY_MAP );
             Assert.fail( "expecting 'invalid content' error" );
 		}
-		catch ( InvalidMappingException expected ) {
+		catch ( InvalidMappingException | AnnotationException expected ) {
 			// expected condition
 		}
 		catch ( PersistenceException expected ) {
 			// expected condition
 		}
-		catch (AnnotationException expected) {
-			// expected condition
-		}
 	}
 
 	public static class PersistenceUnitInfoImpl implements PersistenceUnitInfo {