diff --git a/configure.in b/configure.in
index c4b4e9c9b..b24de0795 100644
--- a/configure.in
+++ b/configure.in
@@ -714,8 +714,6 @@ AC_SUBST(JAVAINC)
 AC_SUBST(JAVADYNAMICLINKING)
 AC_SUBST(JAVALIBRARYPREFIX)
 
-AC_SUBST(ROOT_DIR)ROOT_DIR=`pwd`
-
 #----------------------------------------------------------------
 # Look for Guile
 #----------------------------------------------------------------
@@ -1003,6 +1001,15 @@ AC_SUBST(PIKEDYNAMICLINKING)
 # Miscellaneous
 #----------------------------------------------------------------
 
+# Root directory
+# Translate path for native Windows compilers on Cygwin for use with 'make check'
+ROOT_DIR=`pwd`
+case $ac_sys_system/$ac_sys_release in
+CYGWIN*) ROOT_DIR=`cygpath --mixed $ROOT_DIR`;;
+esac
+
+AC_SUBST(ROOT_DIR)
+
 # Configure SWIG_LIB path
 
 AC_ARG_WITH(swiglibdir,[  --with-swiglibdir=DIR   Put SWIG system-independent libraries into DIR.],