diff --git a/lib/overcommit/git_repo.rb b/lib/overcommit/git_repo.rb
index 1ab1b6b5..284397be 100644
--- a/lib/overcommit/git_repo.rb
+++ b/lib/overcommit/git_repo.rb
@@ -131,12 +131,14 @@ def tracked?(path)
       Overcommit::Utils.execute(%W[git ls-files #{path} --error-unmatch]).success?
     end
 
-    # Returns the names of all files that are tracked by git.
+    # Returns the names of all files that are tracked by git, excluding files
+    # that have been deleted from the working tree.
     #
     # @return [Array<String>] list of absolute file paths
     def all_files
-      `git ls-files`.
-        split(/\n/).
+      deleted_files = `git ls-files --deleted`.split(/\n/)
+
+      (`git ls-files`.split(/\n/) - deleted_files).
         map { |relative_file| File.expand_path(relative_file) }.
         reject { |file| File.directory?(file) } # Exclude submodule directories
     end
diff --git a/spec/overcommit/git_repo_spec.rb b/spec/overcommit/git_repo_spec.rb
index 78f02f98..da4d77d4 100644
--- a/spec/overcommit/git_repo_spec.rb
+++ b/spec/overcommit/git_repo_spec.rb
@@ -293,6 +293,16 @@
 
     it { should include(*%w[tracked staged].map { |file| File.expand_path(file) }) }
     it { should_not include File.expand_path('sub') }
+
+    context 'when a tracked file is deleted but the deletion is not staged' do
+      around do |example|
+        FileUtils.rm 'tracked'
+        example.run
+      end
+
+      it { should_not include File.expand_path('tracked') }
+      it { should include File.expand_path('staged') }
+    end
   end
 
   describe '.initial_commit?' do