diff --git a/lib/pronto/reek.rb b/lib/pronto/reek.rb
index a0dcb7c..977188e 100644
--- a/lib/pronto/reek.rb
+++ b/lib/pronto/reek.rb
@@ -4,7 +4,10 @@
 module Pronto
   class Reek < Runner
     def run
-      files = ruby_patches.map(&:new_file_full_path)
+      files = ruby_patches.map do |patch|
+        patch.new_file_full_path.relative_path_from(Pathname.pwd)
+      end
+
       configuration = ::Reek::Configuration::AppConfiguration.from_path(nil)
 
       smells = files.flat_map do |file|
@@ -37,7 +40,7 @@ def new_message(line, error)
 
     def patch_for_error(error)
       ruby_patches.find do |patch|
-        patch.new_file_full_path.to_s == error.source
+        patch.new_file_full_path.relative_path_from(Pathname.pwd).to_s == error.source
       end
     end
   end
diff --git a/spec/pronto/reek_spec.rb b/spec/pronto/reek_spec.rb
index bac59d4..d06126a 100644
--- a/spec/pronto/reek_spec.rb
+++ b/spec/pronto/reek_spec.rb
@@ -36,8 +36,8 @@ module Pronto
 
       context 'patches with additions to non-ruby files' do
         let(:examiner) { double('examiner', smells: []) }
-        let(:ruby_file) { Pathname.new('ruby_code.rb') }
-        let(:other_file) { Pathname.new('other.stuff') }
+        let(:ruby_file) { Pathname.pwd.join('ruby_code.rb') }
+        let(:other_file) { Pathname.pwd.join('other.stuff') }
         before { ::Reek::Examiner.stub(:new).and_return(examiner) }
 
         let(:patches) do
@@ -51,7 +51,7 @@ module Pronto
 
         it 'calls reek with only the ruby files' do
           subject
-          ::Reek::Examiner.should have_received(:new).with(ruby_file, hash_including(:configuration))
+          ::Reek::Examiner.should have_received(:new).with(Pathname('ruby_code.rb'), hash_including(:configuration))
           ::Reek::Examiner.should_not have_received(:new).with other_file
         end
       end