When exporting org files to .md files using the ox-md.el backend, links like [[file:other-file.org]] are translated to other-file.html. I would expect this to be other-file.md instead. As it stands exporting multiple files to markdown doesn't allow easy interlinking between them. This can be worked around by defin-ing: +BEGIN_SRC :html-extension "md" +END_SRC in the exporting project. But I think this should be fixed in the =org-md-link= function. I am using the following versions GNU Emacs 24.3.1 (i386-mingw-nt6.1.7601) of 2013-03-17 on MARVIN Org-mode version 8.2.5h (8.2.5h-19-g0ceb68-elpa @ c:/Users/a156712/.emacs.d/elpa/org-20140210/) Regards, Mark