diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
index df8ad84b4af..d4b5053a328 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
@@ -22,6 +22,7 @@ import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
  */
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.trim;
 
 import java.io.UnsupportedEncodingException;
 import java.text.Normalizer;
@@ -311,6 +312,29 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 					}
 				}
 
+				Set<String> treatReferencesAsLogical = myConfig.getTreatReferencesAsLogical();
+				if (treatReferencesAsLogical != null) {
+					boolean isLogical = false;
+					for (String nextLogicalRef : treatReferencesAsLogical) {
+						nextLogicalRef = trim(nextLogicalRef);
+						if (nextLogicalRef.charAt(nextLogicalRef.length() - 1) == '*') {
+							if (nextId.getValue().startsWith(nextLogicalRef.substring(0, nextLogicalRef.length() -1))) {
+								isLogical = true;
+								break;
+							}
+						} else {
+							if (nextId.getValue().equals(nextLogicalRef)) {
+								isLogical = true;
+								break;
+							}
+						}
+					}
+					
+					if (isLogical) {
+						continue;
+					}
+				}
+				
 				String baseUrl = nextId.getBaseUrl();
 				String typeString = nextId.getResourceType();
 				if (isBlank(typeString)) {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
index 470105ea099..675cae7cb5c 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
@@ -42,6 +42,8 @@ public class DaoConfig {
 	 * </ul>
 	 */
 	public static final Set<String> DEFAULT_LOGICAL_BASE_URLS = Collections.unmodifiableSet(new HashSet<String>(Arrays.asList(
+			"http://hl7.org/fhir/ValueSet/*",
+			"http://hl7.org/fhir/CodeSystem/*",
 			"http://hl7.org/fhir/valueset-*",
 			"http://hl7.org/fhir/codesystem-*",
 			"http://hl7.org/fhir/StructureDefinition/*")));
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java
index 89cb786d40b..d066eb2b729 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java
@@ -75,6 +75,12 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 	 */
 	@Test
 	public void testBuiltInLogicalReferences() throws IOException {
+		myDaoConfig.getTreatReferencesAsLogical().add("http://phr.kanta.fi/fiphr-vs-*");
+		
+		ValueSet vsBodySite = loadResourceFromClasspath(ValueSet.class, "/issue534/fiphr-vs-bodysite.xml");
+		myValueSetDao.create(vsBodySite, mySrd);
+		ValueSet vsObsMethod = loadResourceFromClasspath(ValueSet.class, "/issue534/fiphr-vs-observationmethod.xml");
+		myValueSetDao.create(vsObsMethod, mySrd);
 		
 		StructureDefinition sd = loadResourceFromClasspath(StructureDefinition.class, "/issue534/bw_profile_snapshot.xml");
 		myStructureDefinitionDao.create(sd, mySrd);
@@ -93,6 +99,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 	@After
 	public final void after() {
 		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
+		myDaoConfig.setTreatReferencesAsLogical(new DaoConfig().getTreatReferencesAsLogical());
 	}
 	
 	
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/issue534/fiphr-vs-bodysite.xml b/hapi-fhir-jpaserver-base/src/test/resources/issue534/fiphr-vs-bodysite.xml
index 5b31d4f503e..391c002e3f1 100644
--- a/hapi-fhir-jpaserver-base/src/test/resources/issue534/fiphr-vs-bodysite.xml
+++ b/hapi-fhir-jpaserver-base/src/test/resources/issue534/fiphr-vs-bodysite.xml
@@ -1,5 +1,4 @@
 <ValueSet>
-    <id value="ce86ecda-449a-4549-9b23-da29385d842a" />
     <meta>
         <versionId value="1" />
         <lastUpdated value="2017-02-23T08:25:27.174+00:00" />
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/issue534/fiphr-vs-observationmethod.xml b/hapi-fhir-jpaserver-base/src/test/resources/issue534/fiphr-vs-observationmethod.xml
index 577d16d45e0..44926aecfb8 100644
--- a/hapi-fhir-jpaserver-base/src/test/resources/issue534/fiphr-vs-observationmethod.xml
+++ b/hapi-fhir-jpaserver-base/src/test/resources/issue534/fiphr-vs-observationmethod.xml
@@ -1,5 +1,4 @@
 <ValueSet>
-    <id value="cace1036-1195-49f4-981e-9e8f3f95ef27" />
     <meta>
         <versionId value="5" />
         <lastUpdated value="2017-03-02T14:04:07.769+00:00" />