diff --git a/configure.ac b/configure.ac
index f2d3c24839..0119ec2246 100644
--- a/configure.ac
+++ b/configure.ac
@@ -816,6 +816,10 @@ fi
 dnl check if we can include both GL and GLES2 at the same time
 if test "x$HAVE_GL" = "xyes" -a "x$HAVE_GLES2" = "xyes"; then
   GL_INCLUDES="
+#ifdef __GNUC__
+#  pragma GCC diagnostic push
+#  pragma GCC diagnostic ignored \"-Wredundant-decls\"
+#endif
 #ifndef GL_GLEXT_PROTOTYPES
 #define GL_GLEXT_PROTOTYPES 1
 #endif
@@ -839,11 +843,12 @@ if test "x$HAVE_GL" = "xyes" -a "x$HAVE_GLES2" = "xyes"; then
 #   include <GL/glext.h>
 #  endif
 # endif
+int main (int argc, char **argv) { return 0; }
 "
   AC_MSG_CHECKING([whether it is possible to include both GL and GLES2 headers])
-  save_CPPFLAGS="$CPPFLAGS"
-  CPPFLAGS="$CPPFLAGS $ERROR_CFLAGS"
-  AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[$GL_INCLUDES]], [[
+  save_CFLAGS="$CFLAGS"
+  CFLAGS="$CFLAGS $GL_CFLAGS $GLES2_CFLAGS $WARNING_CFLAGS $ERROR_CFLAGS"
+  AC_COMPILE_IFELSE([AC_LANG_SOURCE([[$GL_INCLUDES]], [[
     #if !defined(GL_FALSE)
     #error Failed to include GL headers
     #endif
@@ -861,7 +866,7 @@ if test "x$HAVE_GL" = "xyes" -a "x$HAVE_GLES2" = "xyes"; then
       HAVE_GLES2=no
     fi
   ])
-  CPPFLAGS="$save_CPPFLAGS"
+  CFLAGS="$save_CFLAGS"
 fi
 
 #dnl Check for OpenGL
diff --git a/gst-libs/gst/gl/gstglapi.h b/gst-libs/gst/gl/gstglapi.h
index dd44b45239..ab1a203f52 100644
--- a/gst-libs/gst/gl/gstglapi.h
+++ b/gst-libs/gst/gl/gstglapi.h
@@ -23,6 +23,13 @@
 
 #include <gst/gl/gstglconfig.h>
 
+/* This mimic GCC behaviour with system headers files even if GL headers may
+ * not be in the system header path. */
+#ifdef __GNUC__
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wredundant-decls"
+#endif
+
 /* OpenGL 2.0 for Embedded Systems */
 #if GST_GL_HAVE_GLES2
 #ifndef GL_GLEXT_PROTOTYPES
@@ -57,6 +64,10 @@
 # endif
 #endif
 
+#ifdef __GNUC__
+#pragma GCC diagnostic pop
+#endif
+
 #ifdef WINAPI
 #define GSTGLAPI WINAPI
 #else