Instead of using relative paths directly, use paths relative to top_srcdir and top_builddir to refer to source files and built files, respectively. Note that the toplevel zlib configure script still does not have any special support for out-of-tree builds. But now you can do (cd contrib/minizip && autoreconf -fis) mkdir -p BUILD/test cp *.c *.h *.in zlib.map configure zlib.3 BUILD cp test/*.c BUILD/test (cd BUILD && ./configure --shared) (cd BUILD && make) mkdir -p BUILD/contrib/minizip cd BUILD/contrib/minizip ../../../contrib/minizip/configure make While at it, move the include path and library path settings to CPPFLAGS and LDFLAGS respectively instead of setting both in CFLAGS. Thanks to Mike Frysinger for advice.