diff --git a/LibGit2Sharp.Tests/CheckoutFixture.cs b/LibGit2Sharp.Tests/CheckoutFixture.cs
index a09802d1f..17d4a0528 100644
--- a/LibGit2Sharp.Tests/CheckoutFixture.cs
+++ b/LibGit2Sharp.Tests/CheckoutFixture.cs
@@ -23,8 +23,9 @@ public void CanCheckoutAnExistingBranch(string branchName)
                 Branch master = repo.Branches["master"];
                 Assert.True(master.IsCurrentRepositoryHead);
 
-                // Hard reset to ensure that working directory, index, and HEAD match
-                repo.Reset(ResetOptions.Hard);
+                // Set the working directory to the current head
+                ResetAndCleanWorkingDirectory(repo);
+
                 Assert.False(repo.Index.RetrieveStatus().IsDirty);
 
                 Branch branch = repo.Branches[branchName];
@@ -55,8 +56,9 @@ public void CanCheckoutAnExistingBranchByName(string branchName)
                 Branch master = repo.Branches["master"];
                 Assert.True(master.IsCurrentRepositoryHead);
 
-                // Hard reset to ensure that working directory, index, and HEAD match
-                repo.Reset(ResetOptions.Hard);
+                // Set the working directory to the current head
+                ResetAndCleanWorkingDirectory(repo);
+
                 Assert.False(repo.Index.RetrieveStatus().IsDirty);
 
                 Branch test = repo.Checkout(branchName);
@@ -84,8 +86,9 @@ public void CanCheckoutAnArbitraryCommit(string commitPointer)
                 Branch master = repo.Branches["master"];
                 Assert.True(master.IsCurrentRepositoryHead);
 
-                // Hard reset to ensure that working directory, index, and HEAD match
-                repo.Reset(ResetOptions.Hard);
+                // Set the working directory to the current head
+                ResetAndCleanWorkingDirectory(repo);
+
                 Assert.False(repo.Index.RetrieveStatus().IsDirty);
 
                 Branch detachedHead = repo.Checkout(commitPointer);
@@ -197,8 +200,9 @@ public void CanForcefullyCheckoutWithStagedChanges()
                 Branch master = repo.Branches["master"];
                 Assert.True(master.IsCurrentRepositoryHead);
 
-                // Hard reset to ensure that working directory, index, and HEAD match
-                repo.Reset(ResetOptions.Hard);
+                // Set the working directory to the current head
+                ResetAndCleanWorkingDirectory(repo);
+
                 Assert.False(repo.Index.RetrieveStatus().IsDirty);
 
                 // Add local change
@@ -335,5 +339,19 @@ private void PopulateBasicRepository(Repository repo)
 
             repo.CreateBranch(otherBranchName);
         }
+
+        /// <summary>
+        /// Reset and clean current working directory. This will ensure that the current
+        /// working directory matches the current Head commit.
+        /// </summary>
+        /// <param name="repo">Repository whose current working directory should be operated on.</param>
+        private void ResetAndCleanWorkingDirectory(Repository repo)
+        {
+            // Reset the index and the working tree.
+            repo.Reset(ResetOptions.Hard);
+
+            // Remove untracked files.
+            repo.Index.CleanWorkingDirectory();
+        }
     }
 }
diff --git a/LibGit2Sharp.Tests/IndexFixture.cs b/LibGit2Sharp.Tests/IndexFixture.cs
index c286da293..50d0d01ba 100644
--- a/LibGit2Sharp.Tests/IndexFixture.cs
+++ b/LibGit2Sharp.Tests/IndexFixture.cs
@@ -82,6 +82,24 @@ public void ReadIndexWithBadParamsFails()
             }
         }
 
+        [Fact]
+        public void CanCleanWorkingDirectory()
+        {
+            TemporaryCloneOfTestRepo path = BuildTemporaryCloneOfTestRepo(StandardTestRepoWorkingDirPath);
+            using (var repo = new Repository(path.RepositoryPath))
+            {
+                // Verify that there are the expected number of entries and untracked files
+                Assert.Equal(6, repo.Index.RetrieveStatus().Count());
+                Assert.Equal(1, repo.Index.RetrieveStatus().Untracked.Count());
+
+                repo.Index.CleanWorkingDirectory();
+
+                // Verify that there are the expected number of entries and 0 untracked files
+                Assert.Equal(5, repo.Index.RetrieveStatus().Count());
+                Assert.Equal(0, repo.Index.RetrieveStatus().Untracked.Count());
+            }
+        }
+
         [Theory]
         [InlineData("1/branch_file.txt", FileStatus.Unaltered, true, FileStatus.Unaltered, true, 0)]
         [InlineData("README", FileStatus.Unaltered, true, FileStatus.Unaltered, true, 0)]
diff --git a/LibGit2Sharp/Core/NativeMethods.cs b/LibGit2Sharp/Core/NativeMethods.cs
index 0d3b2f207..e246920d8 100644
--- a/LibGit2Sharp/Core/NativeMethods.cs
+++ b/LibGit2Sharp/Core/NativeMethods.cs
@@ -157,6 +157,11 @@ internal static extern int git_checkout_head(
             RepositorySafeHandle repo,
             GitCheckoutOpts opts);
 
+        [DllImport(libgit2)]
+        internal static extern int git_checkout_index(
+            RepositorySafeHandle repo,
+            GitCheckoutOpts opts);
+
         [DllImport(libgit2)]
         internal static extern int git_clone(
             out RepositorySafeHandle repo,
diff --git a/LibGit2Sharp/Core/Proxy.cs b/LibGit2Sharp/Core/Proxy.cs
index 179f0bc22..9a7a94897 100644
--- a/LibGit2Sharp/Core/Proxy.cs
+++ b/LibGit2Sharp/Core/Proxy.cs
@@ -188,6 +188,15 @@ public static void git_checkout_head(RepositorySafeHandle repo, GitCheckoutOpts
             }
         }
 
+        public static void git_checkout_index(RepositorySafeHandle repo, GitCheckoutOpts opts)
+        {
+            using (ThreadAffinity())
+            {
+                int res = NativeMethods.git_checkout_index(repo, opts);
+                Ensure.Success(res);
+            }
+        }
+
         #endregion
 
         #region git_clone_
diff --git a/LibGit2Sharp/Index.cs b/LibGit2Sharp/Index.cs
index 8a9f8d4dd..5e3e68cef 100644
--- a/LibGit2Sharp/Index.cs
+++ b/LibGit2Sharp/Index.cs
@@ -338,6 +338,19 @@ public virtual void Remove(IEnumerable<string> paths)
             UpdatePhysicalIndex();
         }
 
+        /// <summary>
+        /// Clean the working tree by removing files that are not under version control.
+        /// </summary>
+        public virtual void CleanWorkingDirectory()
+        {
+            GitCheckoutOpts options = new GitCheckoutOpts
+            {
+                checkout_strategy = CheckoutStrategy.GIT_CHECKOUT_REMOVE_UNTRACKED,
+            };
+
+            Proxy.git_checkout_index(this.repo.Handle, options);
+        }
+
         private IEnumerable<KeyValuePair<string, FileStatus>> PrepareBatch(IEnumerable<string> paths)
         {
             Ensure.ArgumentNotNull(paths, "paths");