Related bug (maybe the same). Reproduction: $ git clone git@xxxxxxxxxx:jekyll/jekyll.git --no-checkout Cloning into 'jekyll'... remote: Counting objects: 41331, done. remote: Compressing objects: 100% (5/5), done. remote: Total 41331 (delta 0), reused 0 (delta 0), pack-reused 41326 Receiving objects: 100% (41331/41331), 11.91 MiB | 9.15 MiB/s, done. Resolving deltas: 100% (26530/26530), done. $ cd jekyll $ git config core.sparsecheckout true $ echo 'CONDUCT.markdown' > .git/info/sparse-checkout $ echo 'Gemfile' >> .git/info/sparse-checkout $ echo 'Rakefile' >> .git/info/sparse-checkout $ echo 'appveyor.yml' >> .git/info/sparse-checkout $ git checkout -- Your branch is up-to-date with 'origin/master'. $ ls CONDUCT.markdown Gemfile Rakefile appveyor.yml lib I was not expecting to see 'lib' in the resulting file list I didn't say so before - I'm on a Mac, with a homebrew installed Git 2.11.0 - Paul