diff --git a/configure.ac b/configure.ac
index 1813cc57..b190e4b1 100644
--- a/configure.ac
+++ b/configure.ac
@@ -88,7 +88,7 @@ VERSION_MICRO=mym4_version_micro
 AC_CONFIG_AUX_DIR([build-aux])
 AC_CONFIG_MACRO_DIR([m4])
 AC_CONFIG_SRCDIR(src/gpgme.h.in)
-AC_CONFIG_HEADER(config.h)
+AC_CONFIG_HEADER(conf/config.h)
 AM_INIT_AUTOMAKE([serial-tests dist-bzip2 no-dist-gzip])
 AM_MAINTAINER_MODE
 AC_CANONICAL_HOST
diff --git a/doc/Makefile.am b/doc/Makefile.am
index db8a1a21..2b4730ee 100644
--- a/doc/Makefile.am
+++ b/doc/Makefile.am
@@ -34,9 +34,9 @@ gpgme_TEXINFOS = uiserver.texi lesser.texi gpl.texi
 
 gpgme.texi : defs.inc
 
-mkdefsinc: mkdefsinc.c Makefile ../config.h
-	$(CC_FOR_BUILD) -I. -I.. -I$(srcdir) $(AM_CPPFLAGS) \
-	   -o $@ $(srcdir)/mkdefsinc.c
+mkdefsinc: mkdefsinc.c Makefile $(top_builddir)/conf/config.h
+	$(CC_FOR_BUILD) -I. -I$(top_builddir)/conf  -I$(srcdir) \
+	   $(AM_CPPFLAGS) -o $@ $(srcdir)/mkdefsinc.c
 
 dist-hook: defsincdate
 
diff --git a/lang/python/Makefile.am b/lang/python/Makefile.am
index 6df17ceb..6988faf4 100644
--- a/lang/python/Makefile.am
+++ b/lang/python/Makefile.am
@@ -34,7 +34,7 @@ prepare: copystamp
 # distutils are not VPATH-aware.
 copystamp:
 	ln -sf "$(top_srcdir)/src/data.h" .
-	ln -sf "$(top_builddir)/config.h" .
+	ln -sf "$(top_builddir)/conf/config.h" .
 	ln -sf "$(srcdir)/src" gpg
 	touch $@