diff --git a/Makefile.am b/Makefile.am
--- a/Makefile.am
+++ b/Makefile.am
@@ -7,7 +7,8 @@
 	LICENSE \
 	m4/lx_check_cplex.m4 \
 	m4/lx_check_glpk.m4 \
-	m4/lx_check_soplex.m4
+	m4/lx_check_soplex.m4 \
+	CMakeLists.txt
 
 pkgconfigdir = $(libdir)/pkgconfig
 lemondir = $(pkgincludedir)
@@ -44,13 +45,7 @@
 	build-aux/install-sh \
 	build-aux/ltmain.sh \
 	build-aux/missing \
-	doc/Makefile.in \
-	doc/doxygen.log \
-	Makefile.in \
-	lemon/Makefile.in \
-	test/Makefile.in \
-	benchmark/Makefile.in \
-	demo/Makefile.in
+	doc/doxygen.log
 
 mrproper:
 	$(MAKE) $(AM_MAKEFLAGS) maintainer-clean
diff --git a/benchmark/Makefile.am b/benchmark/Makefile.am
--- a/benchmark/Makefile.am
+++ b/benchmark/Makefile.am
@@ -1,6 +1,3 @@
-EXTRA_DIST += \
-        benchmark/Makefile
-
 if WANT_BENCHMARK
 
 noinst_HEADERS +=
diff --git a/demo/Makefile.am b/demo/Makefile.am
--- a/demo/Makefile.am
+++ b/demo/Makefile.am
@@ -1,5 +1,5 @@
 EXTRA_DIST += \
-	demo/Makefile
+	demo/CMakeLists.txt
 
 if WANT_DEMO
 
@@ -13,4 +13,3 @@
 demo_arg_parser_demo_SOURCES = demo/arg_parser_demo.cc
 demo_graph_to_eps_demo_SOURCES = demo/graph_to_eps_demo.cc
 demo_lgf_demo_SOURCES = demo/lgf_demo.cc
-
diff --git a/doc/Makefile.am b/doc/Makefile.am
--- a/doc/Makefile.am
+++ b/doc/Makefile.am
@@ -1,5 +1,4 @@
 EXTRA_DIST += \
-	doc/Makefile \
 	doc/Doxyfile.in \
 	doc/coding_style.dox \
 	doc/dirs.dox \
diff --git a/lemon/Makefile.am b/lemon/Makefile.am
--- a/lemon/Makefile.am
+++ b/lemon/Makefile.am
@@ -1,6 +1,6 @@
 EXTRA_DIST += \
-	lemon/Makefile \
-	lemon/lemon.pc.in
+	lemon/lemon.pc.in \
+	lemon/CMakeLists.txt
 
 pkgconfig_DATA += lemon/lemon.pc
 
diff --git a/test/Makefile.am b/test/Makefile.am
--- a/test/Makefile.am
+++ b/test/Makefile.am
@@ -1,5 +1,5 @@
 EXTRA_DIST += \
-	test/Makefile
+	test/CMakeLists.txt
 
 noinst_HEADERS += \
 	test/digraph_test.h \
diff --git a/tools/Makefile.am b/tools/Makefile.am
--- a/tools/Makefile.am
+++ b/tools/Makefile.am
@@ -1,6 +1,3 @@
-EXTRA_DIST += \
-	tools/Makefile
-
 if WANT_TOOLS
 
 bin_PROGRAMS +=