diff --git a/Makefile.in b/Makefile.in
index 76356126c38..342dc9f97e9 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -75,9 +75,6 @@ tools/wmc tools/wrc: tools
 tools tools/wmc tools/wrc: libs/wine
 tools/widl tools/wmc tools/wrc: libs/wpp
 
-$(MAKEDEP): include/config.h
-	@cd $(TOOLSDIR)/tools && $(MAKE) makedep$(TOOLSEXT)
-
 # Misc rules
 
 TAGSFLAGS = --langmap='c:+.idl.l.rh,make:(Make*.in)'
diff --git a/aclocal.m4 b/aclocal.m4
index 14b6f53dc31..ca52b48aa21 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -218,20 +218,13 @@ wine_fn_depend_rules ()
     ac_alldeps=$[1]
     ac_makedep="\$(MAKEDEP)"
     ac_input=Make.vars.in:$ac_dir/Makefile.in
-    if test $ac_dir != tools
-    then
-        dnl makedep is in tools so tools makefile cannot depend on it
-        ac_alldeps="$[1] $ac_makedep"
-    else
-        ac_alldeps="$[1] include/config.h"
-    fi
     case $[1] in
       *.in) ac_input=$ac_input:$[1] ;;
       *) ac_makedep="$[1] $ac_makedep" ;;
     esac
 
     wine_fn_append_rule \
-"$ac_dir/Makefile: $ac_dir/Makefile.in Make.vars.in config.status $ac_alldeps
+"$ac_dir/Makefile: $ac_dir/Makefile.in Make.vars.in config.status $ac_alldeps \$(MAKEDEP)
 	@./config.status --file $ac_dir/Makefile:$ac_input && cd $ac_dir && \$(MAKE) depend
 depend: $ac_dir/depend
 .PHONY: $ac_dir/depend
diff --git a/configure b/configure
index 103800d5ec9..8277d3c67f4 100755
--- a/configure
+++ b/configure
@@ -16135,19 +16135,13 @@ wine_fn_depend_rules ()
     ac_alldeps=$1
     ac_makedep="\$(MAKEDEP)"
     ac_input=Make.vars.in:$ac_dir/Makefile.in
-    if test $ac_dir != tools
-    then
-                ac_alldeps="$1 $ac_makedep"
-    else
-        ac_alldeps="$1 include/config.h"
-    fi
     case $1 in
       *.in) ac_input=$ac_input:$1 ;;
       *) ac_makedep="$1 $ac_makedep" ;;
     esac
 
     wine_fn_append_rule \
-"$ac_dir/Makefile: $ac_dir/Makefile.in Make.vars.in config.status $ac_alldeps
+"$ac_dir/Makefile: $ac_dir/Makefile.in Make.vars.in config.status $ac_alldeps \$(MAKEDEP)
 	@./config.status --file $ac_dir/Makefile:$ac_input && cd $ac_dir && \$(MAKE) depend
 depend: $ac_dir/depend
 .PHONY: $ac_dir/depend
@@ -17449,9 +17443,12 @@ fi
 
 if test "x$enable_tools" != xno
 then
-    wine_fn_append_rule "\$(MAKEDEP): tools/Makefile
+    ac_config_commands="$ac_config_commands tools"
+
+    wine_fn_append_rule "tools/makedep$ac_exeext: tools/makedep.c include/config.h
+	\$(CC) \$(ALLCFLAGS) -o \$@ $srcdir/tools/makedep.c \$(LDFLAGS)
 clean:: __clean__
-	\$(RM) tools/makedep\$(EXEEXT)"
+	\$(RM) tools/makedep$ac_exeext"
 fi
 
 if test -n "$with_wine64"
@@ -18214,6 +18211,7 @@ do
     "Make.rules") CONFIG_FILES="$CONFIG_FILES Make.rules" ;;
     "Makefile") CONFIG_COMMANDS="$CONFIG_COMMANDS Makefile" ;;
     "Make.tmp") CONFIG_FILES="$CONFIG_FILES Make.tmp:Make.vars.in:Makefile.in" ;;
+    "tools") CONFIG_COMMANDS="$CONFIG_COMMANDS tools" ;;
 
   *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
   esac
@@ -18862,6 +18860,7 @@ $as_echo "$as_me: creating dlls/wineps.drv/data" >&6;}; as_dir="dlls/wineps.drv/
     "include/wine":C) test -d "include/wine" || { { $as_echo "$as_me:${as_lineno-$LINENO}: creating include/wine" >&5
 $as_echo "$as_me: creating include/wine" >&6;}; as_dir="include/wine"; as_fn_mkdir_p; } ;;
     "Makefile":C) wine_fn_output_makefile Makefile ;;
+    "tools":C) as_dir=tools; as_fn_mkdir_p ;;
 
   esac
 done # for ac_tag
diff --git a/configure.ac b/configure.ac
index b3d47ddda36..63435d220cf 100644
--- a/configure.ac
+++ b/configure.ac
@@ -3492,10 +3492,12 @@ fi
 
 if test "x$enable_tools" != xno
 then
+    AC_CONFIG_COMMANDS([tools],[AS_MKDIR_P(tools)])
     WINE_APPEND_RULE(
-[\$(MAKEDEP): tools/Makefile
+[tools/makedep$ac_exeext: tools/makedep.c include/config.h
+	\$(CC) \$(ALLCFLAGS) -o \$@ $srcdir/tools/makedep.c \$(LDFLAGS)
 clean:: __clean__
-	\$(RM) tools/makedep\$(EXEEXT)])
+	\$(RM) tools/makedep$ac_exeext])
 fi
 
 if test -n "$with_wine64"
diff --git a/tools/Makefile.in b/tools/Makefile.in
index 17d70f2ef30..2cf9165520a 100644
--- a/tools/Makefile.in
+++ b/tools/Makefile.in
@@ -35,13 +35,10 @@ INSTALLDIRS = \
 
 UPDATE_DESKTOP_DATABASE = update-desktop-database
 
-all: makedep$(EXEEXT) $(PROGRAMS)
+all: $(PROGRAMS)
 
 @MAKE_RULES@
 
-makedep $(EXEEXT:%=makedep%): makedep.o
-	$(CC) $(CFLAGS) -o $@ makedep.o $(LDFLAGS)
-
 make_ctests$(EXEEXT): make_ctests.o
 	$(CC) $(CFLAGS) -o $@ make_ctests.o $(LDFLAGS)
 
@@ -77,5 +74,3 @@ uninstall::
 		$(DESTDIR)$(mandir)/de.UTF-8/man$(prog_manext)/winemaker.$(prog_manext) \
 		$(DESTDIR)$(mandir)/fr.UTF-8/man$(prog_manext)/winemaker.$(prog_manext)
 	-$(UPDATE_DESKTOP_DATABASE)
-
-depend: makedep$(EXEEXT)