Since cygwin has pushed up its libtool to 2.2.6 and Guile uses libtool 1.5.x, this mismatch can cause a compilation failure. To work around this, you can try the following I have attached 5 small patches configure.in.patch, Makefile.am.patch, guile.c.patch, srfi-14.c.patch and posix.c.patch. The first three do the upgrade to libtool 2.2.6. The last two fix totally harmless pedantic errors that could safely be ignored were it not for the -Werror. $ tar xzvf guile-1.8.5.tar.gz $ cd guile-1.8.5 $ cp ../Makefile.am.patch ../configure.in.patch . $ patch < Makefile.am.patch $ patch < configure.in.patch $ cd libguile $ cp ../../srfi-14.c.patch ../../posix.c.patch ../../guile.c.patch . $ patch < srfi-14.c.patch $ patch < posix.c.patch $ patch < guile.c.patch $ cd .. $ libtoolize $ aclocal $ autoconf $ ./configure && make The shell scripts that call the standalone tests in "make check" hang for some reason. Also, you still get the "freeze on ^D in the REPL" bug that has been a longstanding cygwin mis-feature. Thanks, Mike Gran