diff --git a/configure.ac b/configure.ac
index 1717df2a7a..b16e1f8fa2 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1327,6 +1327,9 @@ GST_GL_HAVE_GLCHAR=0
 GST_GL_HAVE_GLSIZEIPTR=0
 GST_GL_HAVE_GLINTPTR=0
 
+old_CFLAGS=$CFLAGS
+CFLAGS="$GL_CFLAGS $CFLAGS"
+
 AC_CHECK_TYPES(GLeglImageOES, [], [], [[$GL_INCLUDES]])
 if test "x$ac_cv_type_GLeglImageOES" = "xyes"; then
   GST_GL_HAVE_GLEGLIMAGEOES=1
@@ -1347,6 +1350,8 @@ if test "x$ac_cv_type_GLintptr" = "xyes"; then
   GST_GL_HAVE_GLINTPTR=1
 fi
 
+CFLAGS=$old_CFLAGS
+
 GL_CONFIG_DEFINES="$GL_CONFIG_DEFINES
 #define GST_GL_HAVE_GLEGLIMAGEOES $GST_GL_HAVE_GLEGLIMAGEOES
 #define GST_GL_HAVE_GLCHAR $GST_GL_HAVE_GLCHAR