diff --git a/Makefile.am b/Makefile.am
index 828ecb74ca..81ee29e1f1 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -2,10 +2,10 @@ include $(top_srcdir)/config/common.am
 
 ACLOCAL_AMFLAGS = -I m4 -I config
 
-DISTCLEANFILES += lyx.1 config.status config.cache config.log
+DISTCLEANFILES += lyx.1
 
-MAINTAINERCLEANFILES += $(srcdir)/aclocal.m4 \
-	$(srcdir)/configure
+MAINTAINERCLEANFILES += $(srcdir)/aclocal.m4 $(srcdir)/configure \
+	$(srcdir)/config.h.in
 
 DIST_SUBDIRS = m4 config development intl po boost src sourcedoc lib
 
diff --git a/src/Makefile.am b/src/Makefile.am
index 297a296e0e..722ba4dd90 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -4,8 +4,6 @@ include $(top_srcdir)/config/common.am
 
 DISTCLEANFILES += config.h libintl.h
 
-MAINTAINERCLEANFILES += $(srcdir)/config.h.in
-
 AM_CPPFLAGS += $(PCH_FLAGS) -I$(top_srcdir)/src $(BOOST_INCLUDES)
 
 if BUILD_CLIENT_SUBDIR
@@ -14,8 +12,7 @@ endif
 
 SUBDIRS = support frontends . $(CLIENT) tex2lyx
 
-EXTRA_DIST = config.h.in \
-	Section.h \
+EXTRA_DIST = Section.h \
 	Section.cpp \
 	Variables.cpp \
 	Variables.h \
@@ -188,7 +185,6 @@ HEADERFILESCORE = \
 	ColorCode.h \
 	Color.h \
 	CompletionList.h \
-	config.h.in \
 	ConverterCache.h \
 	Converter.h \
 	CoordCache.h \