diff --git a/Makefile.am b/Makefile.am
index a6221e91..5b52d1a3 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -96,6 +96,15 @@ check-local: configure-documentation
 
 configure-documentation:
 	$(AM_V_CHKOPTS)$(top_srcdir)/script/check-cmdline-options-doc.sh \
-		--program "$(top_srcdir)/configure" --text-doc "$(top_srcdir)/INSTALL-WMAKER"
+		--program "$(top_srcdir)/configure" --text-doc "$(top_srcdir)/INSTALL-WMAKER" \
+		--ignore-prg 'with-PACKAGE,without-PACKAGE # only template names from Autoconf' \
+		--ignore-prg 'program-prefix,program-suffix,program-transform-name # in INSTALL' \
+		--ignore-prg 'version,quiet,srcdir,build,host,cache-file,no-create # in INSTALL' \
+		--ignore-prg 'enable-silent-rules,disable-silent-rules # should be in INSTALL' \
+		--ignore-prg 'enable-dependency-tracking,disable-dependency-tracking # in INSTALL' \
+		--ignore-prg 'enable-shared,enable-static # should be in INSTALL' \
+		--ignore-prg 'disable-option-checking,enable-fast-install # should be in INSTALL' \
+		--ignore-prg 'disable-libtool-lock,with-pic,with-gnu-ld,with-sysroot # for libtool' \
+		--ignore-prg 'with-x # no use, it would not work without X'
 
 .PHONY: configure-documentation
diff --git a/script/check-cmdline-options-doc.sh b/script/check-cmdline-options-doc.sh
index 76ad9f79..ff4a4be9 100755
--- a/script/check-cmdline-options-doc.sh
+++ b/script/check-cmdline-options-doc.sh
@@ -51,6 +51,8 @@ print_help() {
     echo "$0: check program's list of options against its documentation"
     echo "Usage: $0 options..."
     echo "valid options are:"
+    echo "  --ignore-prg arg  : ignore option '--arg' from program's output"
+    echo "                (syntax: 'arg1,arg2,... # reason', args without leading '--')"
     echo "  --man-page file   : program's documentation file, in man format"
     echo "  --program name    : name of the program to run with '--help'"
     echo "  --text-doc file   : program's documentation file, in plain text format"
@@ -60,6 +62,16 @@ print_help() {
 # Extract command line arguments
 while [ $# -gt 0 ]; do
     case $1 in
+        --ignore-prg)
+            shift
+            echo "$1" | grep '#' > /dev/null || echo "Warning: no reason provided for --ignore-prg on \"$1\"" >&2
+            for arg in `echo "$1" | sed -e 's/#.*$// ; s/,/ /g' `
+            do
+                ignore_arg_program="$ignore_arg_program
+--$arg"
+            done
+          ;;
+
 	--man-page)
             shift
             [ -z "$man_page$text_doc" ] || arg_error "only 1 documentation file can be used (option: --man-page)"
@@ -112,6 +124,17 @@ prog_options=`$prog_name --help | sed -n '/^[ \t]*-/ { s/^[ \t]*// ; s/^-[^-],[
 
 [ "x$prog_options" = "x" ] && arg_error "program '$prog_name --help' did not return any option"
 
+# We filter options that user wants us to, but we warn if the user asked to filter an option that is
+# not actually present, to make sure his command line invocation stays up to date
+for filter in $ignore_arg_program
+do
+  if echo "$prog_options" | grep "^$filter\$" > /dev/null ; then
+    prog_options=`echo "$prog_options" | grep -v "^$filter\$" `
+  else
+    echo "Warning: program's option does not contain \"$filter\", specified in \"--ignore-prg\""
+  fi
+done
+
 
 if [ -n "$man_page" ]; then
   # In the man page format, the options must be grouped in the section "OPTIONS"