diff --git a/tools/perf/Makefile.config b/tools/perf/Makefile.config
index 16bea51f0bcd9..71442c54c25f4 100644
--- a/tools/perf/Makefile.config
+++ b/tools/perf/Makefile.config
@@ -663,14 +663,17 @@ ifndef NO_BPF_SKEL
   $(call feature_check,clang-bpf-co-re)
   ifeq ($(feature-clang-bpf-co-re), 0)
     dummy := $(error: ERROR: BPF skeletons unsupported. clang too old/not installed or build with NO_BPF_SKEL=1.)
-  else
-    ifeq ($(filter -DHAVE_LIBBPF_SUPPORT, $(CFLAGS)),)
-      dummy := $(error: ERROR: BPF skeletons unsupported. BPF skeleton support requires libbpf or build with NO_BPF_SKEL=1.)
-    else
-      $(call detected,CONFIG_PERF_BPF_SKEL)
-      CFLAGS += -DHAVE_BPF_SKEL
-    endif
   endif
+  ifeq ($(filter -DHAVE_LIBBPF_SUPPORT, $(CFLAGS)),)
+    dummy := $(error: ERROR: BPF skeletons unsupported. BPF skeleton support requires libbpf or build with NO_BPF_SKEL=1.)
+  endif
+  host_byte_order=$(echo ""|$(HOSTCC) -dM -E -|grep __BYTE_ORDER__)
+  target_byte_order=$(echo ""|$(CC) -dM -E -|grep __BYTE_ORDER__)
+  ifneq ($(host_byte_order), $(target_byte_order))
+    $(warning Possibly mismatched host and target endianness may break BPF skeletons)
+  endif
+  $(call detected,CONFIG_PERF_BPF_SKEL)
+  CFLAGS += -DHAVE_BPF_SKEL
 endif
 
 dwarf-post-unwind := 1