diff --git a/src/run_autoconfig b/src/run_autoconfig
index df3b9e9ee1d6aa096921b840eefc5c32e72ea25c..57a740b3021938757ad78cf8f7ec37ee4937aa1c 100755
--- a/src/run_autoconfig
+++ b/src/run_autoconfig
@@ -6,14 +6,13 @@ need_to_make_depend=no
 
 fix()
 {
-  if [ -d $1 ]; then
-    echo "Running autoconf in $1"
-    ( cd $1 ; autoconf )
-  fi
-
   if [ -f $1/acconfig.h ]; then
+    # autoheader runs autoconf
     echo "Running autoheader in $1"
     ( cd $1 ; autoheader )
+  elif [ -f $1/configure.in ]; then
+    echo "Running autoconf in $1"
+    ( cd $1 ; autoconf )
   fi
 
   if [ ! -f $1/dependencies ]; then