diff --git a/NzbDrone.Core.Test/MediaFileProviderTests.cs b/NzbDrone.Core.Test/MediaFileProviderTests.cs
index cc0c63562..95877762b 100644
--- a/NzbDrone.Core.Test/MediaFileProviderTests.cs
+++ b/NzbDrone.Core.Test/MediaFileProviderTests.cs
@@ -359,5 +359,47 @@ namespace NzbDrone.Core.Test
             //Assert
             Assert.AreEqual(expectedName, result);
         }
+
+        [Test]
+        public void CleanEpisodesWithNonExistantFiles()
+        {
+            //Setup
+            var episodes = Builder<Episode>.CreateListOfSize(10).Build();
+
+            var mocker = new AutoMoqer();
+            var database = MockLib.GetEmptyDatabase(true);
+            mocker.SetConstant(database);
+            database.InsertMany(episodes);
+
+            //Act
+            mocker.Resolve<MediaFileProvider>().CleanEpisodesWithNonExistantFiles();
+            var result = database.Fetch<Episode>();
+
+            //Assert
+            result.Should().HaveSameCount(episodes);
+            result.Should().OnlyContain(e => e.EpisodeFileId == 0);
+        }
+
+        [Test]
+        public void DeleteOrphanedEpisodeFiles()
+        {
+            //Setup
+            var episodeFiles = Builder<EpisodeFile>.CreateListOfSize(10).Build();
+            var episodes = Builder<Episode>.CreateListOfSize(5).Build();
+
+            var mocker = new AutoMoqer();
+            var database = MockLib.GetEmptyDatabase(true);
+            mocker.SetConstant(database);
+            database.InsertMany(episodes);
+            database.InsertMany(episodeFiles);
+
+            //Act
+            mocker.Resolve<MediaFileProvider>().DeleteOrphanedEpisodeFiles();
+            var result = database.Fetch<EpisodeFile>();
+
+            //Assert
+            result.Should().HaveCount(5);
+            result.Should().OnlyContain(e => e.EpisodeFileId > 0);
+        }
     }
 }
\ No newline at end of file
diff --git a/NzbDrone.Core/Providers/DiskScanProvider.cs b/NzbDrone.Core/Providers/DiskScanProvider.cs
index 7db6809b5..4db01ffd9 100644
--- a/NzbDrone.Core/Providers/DiskScanProvider.cs
+++ b/NzbDrone.Core/Providers/DiskScanProvider.cs
@@ -196,7 +196,9 @@ namespace NzbDrone.Core.Providers
         /// <param name = "files">list of files to verify</param>
         public virtual void CleanUp(List<EpisodeFile> files)
         {
-            //TODO: remove orphaned files. in files table but not linked to from episode table.
+            _mediaFileProvider.CleanEpisodesWithNonExistantFiles();
+            _mediaFileProvider.DeleteOrphanedEpisodeFiles();
+
             foreach (var episodeFile in files)
             {
                 if (!_diskProvider.FileExists(episodeFile.Path))
diff --git a/NzbDrone.Core/Providers/MediaFileProvider.cs b/NzbDrone.Core/Providers/MediaFileProvider.cs
index d1dc1586a..9d56da9fe 100644
--- a/NzbDrone.Core/Providers/MediaFileProvider.cs
+++ b/NzbDrone.Core/Providers/MediaFileProvider.cs
@@ -74,6 +74,26 @@ namespace NzbDrone.Core.Providers
             return new FileInfo(path);
         }
 
+        public virtual void CleanEpisodesWithNonExistantFiles()
+        {
+            _database.Execute(@"UPDATE Episodes SET EpisodeFileId = 0
+                                WHERE EpisodeFileId IN
+                                (SELECT Episodes.EpisodeFileId FROM Episodes
+                                LEFT OUTER JOIN EpisodeFiles
+                                ON Episodes.EpisodeFileId = EpisodeFiles.EpisodeFileId
+                                WHERE Episodes.EpisodeFileId > 0 AND EpisodeFiles.EpisodeFileId IS null)");
+        }
+
+        public virtual void DeleteOrphanedEpisodeFiles()
+        {
+            _database.Execute(@"DELETE FROM EpisodeFiles
+                                WHERE EpisodeFileId IN
+                                (SELECT EpisodeFiles.EpisodeFileId FROM EpisodeFiles
+                                LEFT OUTER JOIN Episodes
+                                ON EpisodeFiles.EpisodeFileId = Episodes.EpisodeFileId
+                                WHERE Episodes.EpisodeFileId IS null)");
+        }
+
         public virtual string GetNewFilename(IList<Episode> episodes, string seriesTitle, QualityTypes quality)
         {
             var separatorStyle = EpisodeSortingHelper.GetSeparatorStyle(_configProvider.SeparatorStyle);