Creating additional branches in history seems to slow down the 'git annex unused' command quadratically, even if the location of the branches should be irrelevant as far as unused data goes. This was tested on: $ git annex version git-annex version: 3.20130216 local repository version: 3 default repository version: 3 supported repository versions: 3 upgrade supported from repository versions: 0 1 2 What steps will reproduce the problem? $ mkdir a $ cd a $ git init $ git annex init $ i=0 ; while test $i -lt 1000; do dd if=/dev/urandom of=$i.img bs=1M count=1; i=$(($i+1)); done $ git annex add . $ git commit -m"foo" $ git rm 1* $ git commit -m"bar" $ git log --oneline --decorate ffcca3a (HEAD, master) bar 3e7793d foo $ time -p git annex unused unused . (checking for unused data...) (checking master...) (...) real 0.76 user 0.40 sys 0.06 git commit --allow-empty -m"baz" $ git log --oneline --decorate 4390c32 (HEAD, master) baz ffcca3a bar 3e7793d foo $ time -p git annex unused unused . (checking for unused data...) (checking master...) (...) real 0.75 user 0.38 sys 0.07 $ git branch boo HEAD^ $ time -p git annex unused unused . (checking for unused data...) (checking boo...) (checking master...) (...) real 1.29 user 0.62 sys 0.08 arand@mas:~/tmp/more/a(master)$ git branch beeboo HEAD^ 4390c32 (HEAD, master) baz ffcca3a (boo, beeboo) bar 3e7793d foo arand@mas:~/tmp/more/a(master)$ time -p git annex unused unused . (checking for unused data...) (checking beeboo...) (checking master...) (...) real 2.50 user 1.12 sys 0.14 $ git branch -d boo beeboo $ git log --oneline --decorate 4390c32 (HEAD, master) baz ffcca3a bar 3e7793d foo $ time -p git annex unused unused . (checking for unused data...) (checking master...) (...) real 0.77 user 0.42 sys 0.04 What is the expected output? What do you see instead? I would expect the time to be the same in all the above cases. What version of git-annex are you using? On what operating system? $ git annex version git-annex version: 3.20130216 On current Debian sid/experimental