Hello, I am reporting a problem that we discussed today in the thread starting at http://lists.gnu.org/archive/html/libtool/2012-08/msg00010.html The same behavior exists with libtool 2.2.6b and 2.4.2. Looking at the git log, it has likely been there for ever. I am attaching a small testcase. Here's how to use it: tar xfj bug.tar.bz2 cd bug autoreconf -ifv ./configure make [... fails quickly with...] libltdl/lt__private.h:35:23: fatal error: mysubdir/config.h: No such file or directory The issue is that lt__private.h contains #include LT_CONFIG_H and LT_CONFIG_H is set to the entire relative path given in AC_CONFIG_HEADER. So the build cannot find it unless -I$(top_builddir) is added to CPPFLAGS. From what was said in today's discussion, automake adds the path to the config header to CPPFLAGS, so libltdl should just set LT_CONFIG_H to the config header basename without any path. The problem can be worked around by modifying the embedder's project CPPFLAGS as explained above, or by adding this AC_CONFIG_COMMANDS_PRE([LT_CONFIG_H=`expr "$LT_CONFIG_H" : '.*/\(.*\)'`]) Thanks Brice