diff --git a/src/main/java/org/springframework/data/jpa/provider/HibernateUtils.java b/src/main/java/org/springframework/data/jpa/provider/HibernateUtils.java
index 39f8e0258..d8baf0d48 100644
--- a/src/main/java/org/springframework/data/jpa/provider/HibernateUtils.java
+++ b/src/main/java/org/springframework/data/jpa/provider/HibernateUtils.java
@@ -63,7 +63,7 @@ public abstract class HibernateUtils {
 			queryInterface = ClassUtils.forName("org.hibernate.query.Query", classLoader);
 		} catch (Exception o_O) {}
 
-		HIBERNATE_QUERY_INTERFACE = queryInterface;
+		HIBERNATE_QUERY_INTERFACE = queryInterface == null ? type : queryInterface;
 		QUERY_STRING_METHOD = HIBERNATE_QUERY_INTERFACE == null ? null
 				: ReflectionUtils.findMethod(HIBERNATE_QUERY_INTERFACE, "getQueryString");
 	}
@@ -76,10 +76,15 @@ public abstract class HibernateUtils {
 	 */
 	public static String getHibernateQuery(Object query) {
 
-		if (HIBERNATE_QUERY_INTERFACE != null && HIBERNATE_QUERY_INTERFACE.isInstance(query)) {
+		if (HIBERNATE_QUERY_INTERFACE != null && QUERY_STRING_METHOD != null
+				&& HIBERNATE_QUERY_INTERFACE.isInstance(query)) {
 			return String.class.cast(ReflectionUtils.invokeMethod(QUERY_STRING_METHOD, query));
 		}
 
+		if (HIBERNATE_QUERY_INTERFACE != null && !HIBERNATE_QUERY_INTERFACE.isInstance(query)) {
+			query = ((javax.persistence.Query) query).unwrap(HIBERNATE_QUERY_INTERFACE);
+		}
+
 		return ((Query) ReflectionUtils.invokeMethod(GET_HIBERNATE_QUERY, query)).getQueryString();
 	}
 }
diff --git a/src/main/java/org/springframework/data/jpa/repository/query/JpaCountQueryCreator.java b/src/main/java/org/springframework/data/jpa/repository/query/JpaCountQueryCreator.java
index 6eeb3eac3..bbbddb90a 100644
--- a/src/main/java/org/springframework/data/jpa/repository/query/JpaCountQueryCreator.java
+++ b/src/main/java/org/springframework/data/jpa/repository/query/JpaCountQueryCreator.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2008-2013 the original author or authors.
+ * Copyright 2008-2017 the original author or authors.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -29,6 +29,7 @@ import org.springframework.data.repository.query.parser.PartTree;
  * Special {@link JpaQueryCreator} that creates a count projecting query.
  * 
  * @author Oliver Gierke
+ * @author Marc Lefrançois
  */
 public class JpaCountQueryCreator extends JpaQueryCreator {
 
@@ -59,11 +60,16 @@ public class JpaCountQueryCreator extends JpaQueryCreator {
 	 * @see org.springframework.data.jpa.repository.query.JpaQueryCreator#complete(javax.persistence.criteria.Predicate, org.springframework.data.domain.Sort, javax.persistence.criteria.CriteriaQuery, javax.persistence.criteria.CriteriaBuilder, javax.persistence.criteria.Root)
 	 */
 	@Override
-	@SuppressWarnings({ "unchecked", "rawtypes" })
+	@SuppressWarnings("unchecked")
 	protected CriteriaQuery<? extends Object> complete(Predicate predicate, Sort sort,
 			CriteriaQuery<? extends Object> query, CriteriaBuilder builder, Root<?> root) {
 
-		CriteriaQuery<? extends Object> select = query.select((Expression) builder.count(root));
+		CriteriaQuery<? extends Object> select = query.select(getCountQuery(query, builder, root));
 		return predicate == null ? select : select.where(predicate);
 	}
+
+	@SuppressWarnings("rawtypes")
+	private static Expression getCountQuery(CriteriaQuery<?> query, CriteriaBuilder builder, Root<?> root) {
+		return query.isDistinct() ? builder.countDistinct(root) : builder.count(root);
+	}
 }
diff --git a/src/test/java/org/springframework/data/jpa/repository/query/JpaCountQueryCreatorIntegrationTests.java b/src/test/java/org/springframework/data/jpa/repository/query/JpaCountQueryCreatorIntegrationTests.java
new file mode 100644
index 000000000..52ebce262
--- /dev/null
+++ b/src/test/java/org/springframework/data/jpa/repository/query/JpaCountQueryCreatorIntegrationTests.java
@@ -0,0 +1,76 @@
+/*
+ * Copyright 2017 the original author or authors.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.springframework.data.jpa.repository.query;
+
+import static org.hamcrest.CoreMatchers.*;
+import static org.junit.Assert.*;
+
+import java.lang.reflect.Method;
+import java.util.List;
+
+import javax.persistence.EntityManager;
+import javax.persistence.PersistenceContext;
+import javax.persistence.TypedQuery;
+
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.data.jpa.domain.sample.Role;
+import org.springframework.data.jpa.domain.sample.User;
+import org.springframework.data.jpa.provider.HibernateUtils;
+import org.springframework.data.jpa.provider.PersistenceProvider;
+import org.springframework.data.projection.SpelAwareProxyProjectionFactory;
+import org.springframework.data.repository.Repository;
+import org.springframework.data.repository.core.support.AbstractRepositoryMetadata;
+import org.springframework.data.repository.query.parser.PartTree;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+
+/**
+ * Integration tests for {@link JpaCountQueryCreator}.
+ * 
+ * @author Oliver Gierke
+ */
+@RunWith(SpringJUnit4ClassRunner.class)
+@ContextConfiguration("classpath:infrastructure.xml")
+public class JpaCountQueryCreatorIntegrationTests {
+
+	@PersistenceContext EntityManager entityManager;
+
+	@Test // DATAJPA-1044
+	public void distinctFlagOnCountQueryIssuesCountDistinct() throws Exception {
+
+		Method method = SomeRepository.class.getMethod("findDistinctByRolesIn", List.class);
+
+		PersistenceProvider provider = PersistenceProvider.fromEntityManager(entityManager);
+		JpaQueryMethod queryMethod = new JpaQueryMethod(method,
+				AbstractRepositoryMetadata.getMetadata(SomeRepository.class), new SpelAwareProxyProjectionFactory(), provider);
+
+		PartTree tree = new PartTree("findDistinctByRolesIn", User.class);
+		ParameterMetadataProvider metadataProvider = new ParameterMetadataProvider(entityManager.getCriteriaBuilder(),
+				queryMethod.getParameters(), provider);
+
+		JpaCountQueryCreator creator = new JpaCountQueryCreator(tree, queryMethod.getResultProcessor().getReturnedType(),
+				entityManager.getCriteriaBuilder(), metadataProvider);
+
+		TypedQuery<? extends Object> query = entityManager.createQuery(creator.createQuery());
+
+		assertThat(HibernateUtils.getHibernateQuery(query), startsWith("select distinct count(distinct"));
+	}
+
+	interface SomeRepository extends Repository<User, Long> {
+		void findDistinctByRolesIn(List<Role> roles);
+	}
+}