diff --git a/configure.ac b/configure.ac
--- a/configure.ac
+++ b/configure.ac
@@ -87,6 +87,10 @@
 AC_HEADER_STDC
 AC_CHECK_FUNCS(gettimeofday times ctime_r)
 
+dnl Add dependencies on files generated by configure.
+AC_SUBST([CONFIG_STATUS_DEPENDENCIES],
+  ['$(top_srcdir)/doc/Doxyfile.in $(top_srcdir)/lemon/lemon.pc.in'])
+
 AC_CONFIG_FILES([
 Makefile
 doc/Doxyfile