diff --git a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddIndexTask.java b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddIndexTask.java
index cd4b3305fb9..c47cc2cd64b 100644
--- a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddIndexTask.java
+++ b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddIndexTask.java
@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
 import ca.uhn.fhir.jpa.migrate.JdbcUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.EqualsBuilder;
@@ -78,7 +79,18 @@ public class AddIndexTask extends BaseTableTask {
 
 		String unique = myUnique ? "unique " : "";
 		String columns = String.join(", ", myColumns);
-		String sql = "create " + unique + "index " + myIndexName + " on " + getTableName() + "(" + columns + ")";
+		String mssqlWhereClause = "";
+		if (myUnique && getDriverType() == DriverTypeEnum.MSSQL_2012) {
+			mssqlWhereClause = " WHERE (";
+			for (int i = 0; i <myColumns.size(); i++) {
+				mssqlWhereClause += myColumns.get(i) + " IS NOT NULL ";
+				if (i < myColumns.size() - 1) {
+					mssqlWhereClause += "AND ";
+				}
+			}
+			mssqlWhereClause += ")";
+		}
+		String sql = "create " + unique + "index " + myIndexName + " on " + getTableName() + "(" + columns + ")" + mssqlWhereClause;
 		String tableName = getTableName();
 
 		try {