diff --git a/GNUmakefile b/GNUmakefile
index b829e93b498..a2a630ba9d5 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -32,6 +32,11 @@
 # run "configure" by hand.  But run autogen.sh first, if the source
 # was checked out directly from the repository.
 
+ifneq ($(MSYSTEM),)
+CFG = CONFIG_SITE=$(CURDIR)/nt/mingw-cfg.site
+else
+CFG =
+endif
 
 # If a Makefile already exists, just use it.
 
@@ -70,7 +75,7 @@ configure:
 Makefile: configure
 	@echo >&2 'There seems to be no Makefile in this directory.'
 	@echo >&2 'Running ./configure ...'
-	./configure
+	$(CFG) ./configure
 	@echo >&2 'Makefile built.'
 
 endif
diff --git a/Makefile.in b/Makefile.in
index 6e0f151ea1a..e84090806c3 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -393,9 +393,9 @@ $(MAKEFILE_NAME): config.status $(srcdir)/src/config.in \
 
 config.status: ${srcdir}/configure ${srcdir}/lisp/version.el
 	if [ -x ./config.status ]; then	\
-	    ./config.status --recheck;	\
+	    $(CFG) ./config.status --recheck;	\
 	else				\
-	    $(srcdir)/configure $(CONFIGURE_FLAGS); \
+	    $(CFG) $(srcdir)/configure $(CONFIGURE_FLAGS); \
 	fi
 
 AUTOCONF_INPUTS = $(srcdir)/configure.ac $(srcdir)/aclocal.m4