diff --git a/Makefile.in b/Makefile.in
index eb4d0dac93b..c2bb1ed4caa 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -32,11 +32,11 @@ all: wine
 
 # Rules for re-running configure
 
-config.status: configure
+config.status: $(srcdir)/configure
 	@./config.status --recheck
 
 include/config.h: include/stamp-h
-include/stamp-h: include/config.h.in config.status
+include/stamp-h: $(srcdir)/include/config.h.in config.status
 	@./config.status include/config.h include/stamp-h
 
 # Rules for cleaning
diff --git a/aclocal.m4 b/aclocal.m4
index d6f57905c95..623177258e5 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -219,12 +219,15 @@ wine_fn_depend_rules ()
     ac_makedep="\$(MAKEDEP)"
     ac_input=Make.vars.in:$ac_dir/Makefile.in
     case $[1] in
-      *.in) ac_input=$ac_input:$[1] ;;
-      *) ac_makedep="$[1] $ac_makedep" ;;
+      *.in)
+          ac_input=$ac_input:$[1]
+          test "$srcdir" = . || ac_alldeps="$srcdir/$ac_alldeps" ;;
+      *)
+          ac_makedep="$[1] $ac_makedep" ;;
     esac
 
     wine_fn_append_rule \
-"$ac_dir/Makefile: $ac_dir/Makefile.in Make.vars.in config.status $ac_alldeps \$(MAKEDEP)
+"$ac_dir/Makefile: $srcdir/$ac_dir/Makefile.in $srcdir/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: $ac_dir/depend
@@ -628,7 +631,7 @@ wine_fn_config_makerules ()
     ac_rules=$[1]
     ac_deps=$[2]
     wine_fn_append_rule \
-"$ac_rules: $ac_rules.in $ac_deps config.status
+"$ac_rules: $srcdir/$ac_rules.in $ac_deps config.status
 	@./config.status $ac_rules
 distclean::
 	\$(RM) $ac_rules"
diff --git a/configure b/configure
index 81a474fe998..9953777a90a 100755
--- a/configure
+++ b/configure
@@ -16216,12 +16216,15 @@ wine_fn_depend_rules ()
     ac_makedep="\$(MAKEDEP)"
     ac_input=Make.vars.in:$ac_dir/Makefile.in
     case $1 in
-      *.in) ac_input=$ac_input:$1 ;;
-      *) ac_makedep="$1 $ac_makedep" ;;
+      *.in)
+          ac_input=$ac_input:$1
+          test "$srcdir" = . || ac_alldeps="$srcdir/$ac_alldeps" ;;
+      *)
+          ac_makedep="$1 $ac_makedep" ;;
     esac
 
     wine_fn_append_rule \
-"$ac_dir/Makefile: $ac_dir/Makefile.in Make.vars.in config.status $ac_alldeps \$(MAKEDEP)
+"$ac_dir/Makefile: $srcdir/$ac_dir/Makefile.in $srcdir/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
@@ -16641,7 +16644,7 @@ wine_fn_config_makerules ()
     ac_rules=$1
     ac_deps=$2
     wine_fn_append_rule \
-"$ac_rules: $ac_rules.in $ac_deps config.status
+"$ac_rules: $srcdir/$ac_rules.in $ac_deps config.status
 	@./config.status $ac_rules
 distclean::
 	\$(RM) $ac_rules"
@@ -16677,7 +16680,7 @@ wine_fn_append_rule "
 .INIT: Makefile
 .MAKEFILEDEPS:
 all: Makefile
-Makefile: Makefile.in Make.vars.in Make.rules config.status
+Makefile: $srcdir/Makefile.in $srcdir/Make.vars.in Make.rules config.status
 	@./config.status Make.tmp Makefile"
 
 if test "x$enable_fonts" != xno; then
diff --git a/configure.ac b/configure.ac
index 01246529b6a..aa170640b76 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2667,7 +2667,7 @@ WINE_APPEND_RULE([
 .INIT: Makefile
 .MAKEFILEDEPS:
 all: Makefile
-Makefile: Makefile.in Make.vars.in Make.rules config.status
+Makefile: $srcdir/Makefile.in $srcdir/Make.vars.in Make.rules config.status
 	@./config.status Make.tmp Makefile])
 
 WINE_CONFIG_SYMLINK(fonts,fonts,[marlett.ttf,symbol.ttf,tahoma.ttf,tahomabd.ttf],enable_fonts)
diff --git a/tools/makedep.c b/tools/makedep.c
index f8415c6bca5..32383f4577a 100644
--- a/tools/makedep.c
+++ b/tools/makedep.c
@@ -1363,7 +1363,7 @@ static void output_sources(void)
 
     if (find_src_file( "dlldata.o" ))
     {
-        output( "dlldata.c: $(WIDL) Makefile.in\n" );
+        output( "dlldata.c: $(WIDL) %s\n", src_dir ? strmake("%s/Makefile.in", src_dir ) : "Makefile.in" );
         column = output( "\t$(WIDL) --dlldata-only -o $@" );
         LIST_FOR_EACH_ENTRY( source, &sources, struct incl_file, entry )
             if (source->flags & FLAG_IDL_PROXY) output_filename( source->filename, &column );
@@ -1373,7 +1373,7 @@ static void output_sources(void)
 
     if (is_test)
     {
-        output( "testlist.c: $(MAKECTESTS) Makefile.in\n" );
+        output( "testlist.c: $(MAKECTESTS) %s\n", src_dir ? strmake("%s/Makefile.in", src_dir ) : "Makefile.in" );
         column = output( "\t$(MAKECTESTS) -o $@" );
         LIST_FOR_EACH_ENTRY( source, &sources, struct incl_file, entry )
             if (strendswith( source->name, ".c" ) && !is_generated_idl( source ))