This is my .gitignore as per http://stackoverflow.com/questions/991801/git-ignores-and-maven-targets/995325 so that Win32/Debug directories in various parts of the tree are ignored: https://github.com/jpluimers/atom-table-monitor/blob/master/.gitignore *.~* *.dsk *.local *.identcache Win32/Debug/ ATOMScannerConsole/MAINICON.res ATOMScannerConsole/VERSIONINFO.res SourceTree 1.6.20 shows files in various directories: https://www.dropbox.com/s/tvjdomogrhfuwcu/20150817-SourceTree-not-handling-.gitignore-correctly.png?dl=0 .../bin/Win32/Debug/ .../obj/Win32/Debug/ .../lib/Win32/Debug/ git status doesn't show these: C:\...\Versioned\atom-table-monitor>git status On branch master Your branch is up-to-date with 'origin/master' . Untracked files: (use "git add <file>..." to include in what will be committed) ATOMScannerConsole/bin/ ATOMScannerConsole/lib/ ATOMService/bin/ ATOMService/obj/ nothing added to commit but untracked files present (use "git add" to track) Please fix that.