diff --git a/mysql-test/t/show_check.test b/mysql-test/t/show_check.test
index 341c9039390..6e848695b80 100644
--- a/mysql-test/t/show_check.test
+++ b/mysql-test/t/show_check.test
@@ -761,7 +761,23 @@ DROP VIEW v1;
 DROP PROCEDURE p1;
 DROP FUNCTION f1;
 
---echo End of 5.0 tests.
+#
+# Bug #28808: log_queries_not_using_indexes variable dynamic change is ignored
+#
+flush status;
+show variables like "log_queries_not_using_indexes";
+select 1 from information_schema.tables limit 1;
+show status like 'slow_queries';
+set global log_queries_not_using_indexes=OFF;
+show variables like "log_queries_not_using_indexes";
+select 1 from information_schema.tables limit 1;
+show status like 'slow_queries';
+set global log_queries_not_using_indexes=ON;
+show variables like "log_queries_not_using_indexes";
+select 1 from information_schema.tables limit 1;
+show status like 'slow_queries';
+
+--echo End of 5.0 tests
 
 --disable_result_log
 SHOW AUTHORS;
diff --git a/sql/mysqld.cc b/sql/mysqld.cc
index 10ae466fe4d..6d22047b9db 100644
--- a/sql/mysqld.cc
+++ b/sql/mysqld.cc
@@ -7820,8 +7820,6 @@ static void get_options(int *argc,char **argv)
 
   if (opt_short_log_format)
     opt_specialflag|= SPECIAL_SHORT_LOG_FORMAT;
-  if (opt_log_queries_not_using_indexes)
-    opt_specialflag|= SPECIAL_LOG_QUERIES_NOT_USING_INDEXES;
 
   if (init_global_datetime_format(MYSQL_TIMESTAMP_DATE,
 				  &global_system_variables.date_format) ||
diff --git a/sql/sql_parse.cc b/sql/sql_parse.cc
index aa661b64598..000a0a30de6 100644
--- a/sql/sql_parse.cc
+++ b/sql/sql_parse.cc
@@ -1323,7 +1323,7 @@ void log_slow_statement(THD *thd)
 	thd->variables.long_query_time ||
 	((thd->server_status &
 	  (SERVER_QUERY_NO_INDEX_USED | SERVER_QUERY_NO_GOOD_INDEX_USED)) &&
-	 (specialflag & SPECIAL_LOG_QUERIES_NOT_USING_INDEXES)))
+	 opt_log_queries_not_using_indexes))
     {
       thd->status_var.long_query_count++;
       slow_log_print(thd, thd->query, thd->query_length, start_of_query);
diff --git a/sql/unireg.h b/sql/unireg.h
index 5b73c6e9caa..6c26f30f116 100644
--- a/sql/unireg.h
+++ b/sql/unireg.h
@@ -124,7 +124,7 @@
 #define SPECIAL_NO_HOST_CACHE	512		/* Don't cache hosts */
 #define SPECIAL_SHORT_LOG_FORMAT 1024
 #define SPECIAL_SAFE_MODE	2048
-#define SPECIAL_LOG_QUERIES_NOT_USING_INDEXES 4096 /* Log q not using indexes */
+#define SPECIAL_LOG_QUERIES_NOT_USING_INDEXES 4096 /* Obsolete */
 
 	/* Extern defines */
 #define store_record(A,B) bmove_align((A)->B,(A)->record[0],(size_t) (A)->s->reclength)