diff --git a/ChangeLog b/ChangeLog
index 25ffe0f9ca..108fa35b0a 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,10 @@
+Sun Feb 17 00:52:14 2013  NARUSE, Yui  <naruse@ruby-lang.org>
+
+	* tool/mkconfig.rb: remove prefix from rubyarchdir.
+	  r39267 expands variables, it changes expansion timing,
+	  breaks RbConfig::CONFIG["includedir"] and building
+	  extension libraries with installed ruby.
+
 Sat Feb 16 20:51:17 2013  Kazuki Tsujimoto  <kazuki@callcc.net>
 
 	* vm.c (ENV_IN_HEAP_P): fix off-by-one error.
diff --git a/tool/mkconfig.rb b/tool/mkconfig.rb
index e4a925cd51..92c765499f 100755
--- a/tool/mkconfig.rb
+++ b/tool/mkconfig.rb
@@ -167,7 +167,7 @@ def vars.expand(val, config = self)
   val
 end
 vars["prefix"] = ""
-prefix = vars.expand(vars["rubyarchdir"])
+prefix = vars.expand(vars["rubyarchdir"]).sub!(vars.expand(vars["exec_prefix"]), '')
 print "  TOPDIR = File.dirname(__FILE__).chomp!(#{prefix.dump})\n"
 print "  DESTDIR = ", (drive ? "TOPDIR && TOPDIR[/\\A[a-z]:/i] || " : ""), "'' unless defined? DESTDIR\n"
 print <<'ARCH' if universal