diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/NL1.patch b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/NL1.patch
new file mode 100644
index 000000000..ba5a4fc25
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/NL1.patch
@@ -0,0 +1,10 @@
+diff --git a/NL1 b/NL1
+index 68abad7..b14088c 100644
+--- a/NL1
++++ b/NL1
+@@ -1,4 +1,4 @@
+ a
+-b
++d
+ c
+ 
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/NL1_PostImage b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/NL1_PostImage
new file mode 100644
index 000000000..b14088c04
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/NL1_PostImage
@@ -0,0 +1,4 @@
+a
+d
+c
+
diff --git a/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/NL1_PreImage b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/NL1_PreImage
new file mode 100644
index 000000000..68abad7d9
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/NL1_PreImage
@@ -0,0 +1,4 @@
+a
+b
+c
+
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java
index 5513b4460..a0a4ddcbf 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java
@@ -178,6 +178,16 @@ public class ApplyCommandTest extends RepositoryTestCase {
 				b.getString(0, b.size(), false));
 	}
 
+	@Test
+	public void testModifyNL1() throws Exception {
+		ApplyResult result = init("NL1");
+		assertEquals(1, result.getUpdatedFiles().size());
+		assertEquals(new File(db.getWorkTree(), "NL1"), result
+				.getUpdatedFiles().get(0));
+		checkFile(new File(db.getWorkTree(), "NL1"),
+				b.getString(0, b.size(), false));
+	}
+
 	private static byte[] readFile(final String patchFile) throws IOException {
 		final InputStream in = DiffFormatterReflowTest.class
 				.getResourceAsStream(patchFile);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java
index 2147a2e5c..6a945e4d3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java
@@ -238,13 +238,10 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
 		if (!isChanged(oldLines, newLines))
 			return; // don't touch the file
 		StringBuilder sb = new StringBuilder();
-		final String eol = rt.size() == 0
-				|| (rt.size() == 1 && rt.isMissingNewlineAtEnd()) ? "\n" : rt //$NON-NLS-1$
-				.getLineDelimiter();
 		for (String l : newLines) {
-			sb.append(l);
-			if (eol != null)
-				sb.append(eol);
+			// don't bother handling line endings - if it was windows, the \r is
+			// still there!
+			sb.append(l).append('\n');
 		}
 		sb.deleteCharAt(sb.length() - 1);
 		FileWriter fw = new FileWriter(f);
@@ -252,7 +249,7 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
 		fw.close();
 	}
 
-	private boolean isChanged(List<String> ol, List<String> nl) {
+	private static boolean isChanged(List<String> ol, List<String> nl) {
 		if (ol.size() != nl.size())
 			return true;
 		for (int i = 0; i < ol.size(); i++)