diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PathCheckoutCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PathCheckoutCommandTest.java
index 243d791..d37f572 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PathCheckoutCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/PathCheckoutCommandTest.java
@@ -47,11 +47,13 @@
 import java.io.File;
 import java.io.IOException;
 
+import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.errors.NoWorkTreeException;
 import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.ObjectReader;
+import org.eclipse.jgit.lib.RepositoryState;
 import org.eclipse.jgit.lib.RepositoryTestCase;
 import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.revwalk.RevCommit;
@@ -243,4 +245,23 @@ public void testCheckoutRepository() throws Exception {
 		assertEquals("1", read(test));
 		assertEquals("a", read(test2));
 	}
+
+	@Test(expected = JGitInternalException.class)
+	public void testCheckoutOfConflictingFileShouldThrow()
+			throws Exception {
+		// Setup
+		git.checkout().setCreateBranch(true).setName("conflict")
+				.setStartPoint(initialCommit).call();
+		writeTrashFile(FILE1, "Conflicting");
+		RevCommit conflict = git.commit().setAll(true)
+				.setMessage("Conflicting change").call();
+
+		git.checkout().setName("master").call();
+
+		git.merge().include(conflict).call();
+		assertEquals(RepositoryState.MERGING, db.getRepositoryState());
+
+		// Now check out the conflicting path
+		git.checkout().addPath(FILE1).call();
+	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
index d8efbe7..57f47a4 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
@@ -64,6 +64,7 @@
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.dircache.DirCacheIterator;
 import org.eclipse.jgit.errors.AmbiguousObjectException;
+import org.eclipse.jgit.errors.UnmergedPathException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Constants;
@@ -284,7 +285,8 @@ protected CheckoutCommand checkoutPaths() throws IOException,
 			startWalk.setRecursive(true);
 			if (!checkoutAllPaths)
 				startWalk.setFilter(PathFilterGroup.createFromStrings(paths));
-			boolean checkoutIndex = startCommit == null && startPoint == null;
+			final boolean checkoutIndex = startCommit == null
+					&& startPoint == null;
 			if (!checkoutIndex)
 				startWalk.addTree(revWalk.parseCommit(getStartPoint())
 						.getTree());
@@ -299,6 +301,11 @@ protected CheckoutCommand checkoutPaths() throws IOException,
 					final FileMode mode = startWalk.getFileMode(0);
 					editor.add(new PathEdit(startWalk.getPathString()) {
 						public void apply(DirCacheEntry ent) {
+							if (checkoutIndex
+									&& ent.getStage() > DirCacheEntry.STAGE_0) {
+								UnmergedPathException e = new UnmergedPathException(ent);
+								throw new JGitInternalException(e.getMessage(), e);
+							}
 							ent.setObjectId(blobId);
 							ent.setFileMode(mode);
 							File file = new File(workTree, ent.getPathString());