diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitAndLogCommandTests.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitAndLogCommandTests.java
index d8fbb95..a62045d 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitAndLogCommandTests.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitAndLogCommandTests.java
@@ -42,14 +42,22 @@
  */
 package org.eclipse.jgit.api;
 
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+
 import org.eclipse.jgit.errors.UnmergedPathException;
+import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.PersonIdent;
+import org.eclipse.jgit.lib.RefUpdate;
 import org.eclipse.jgit.lib.RepositoryTestCase;
 import org.eclipse.jgit.revwalk.RevCommit;
 
 public class CommitAndLogCommandTests extends RepositoryTestCase {
 	public void testSomeCommits() throws NoHeadException, NoMessageException,
-			UnmergedPathException, ConcurrentRefUpdateException {
+			UnmergedPathException, ConcurrentRefUpdateException,
+			JGitInternalException, WrongRepositoryStateException {
 
 		// do 4 commits
 		Git git = new Git(db);
@@ -62,8 +70,8 @@
 
 		// check that all commits came in correctly
 		PersonIdent defaultCommitter = new PersonIdent(db);
-		PersonIdent expectedAuthors[] = new PersonIdent[] {
-				defaultCommitter, committer, author, author };
+		PersonIdent expectedAuthors[] = new PersonIdent[] { defaultCommitter,
+				committer, author, author };
 		PersonIdent expectedCommitters[] = new PersonIdent[] {
 				defaultCommitter, committer, defaultCommitter, committer };
 		String expectedMessages[] = new String[] { "initial commit",
@@ -82,7 +90,8 @@
 
 	// try to do a commit without specifying a message. Should fail!
 	public void testWrongParams() throws UnmergedPathException,
-			NoHeadException, ConcurrentRefUpdateException {
+			NoHeadException, ConcurrentRefUpdateException,
+			JGitInternalException, WrongRepositoryStateException {
 		Git git = new Git(db);
 		try {
 			git.commit().setAuthor(author).call();
@@ -95,7 +104,8 @@
 	// exceptions
 	public void testMultipleInvocations() throws NoHeadException,
 			ConcurrentRefUpdateException, NoMessageException,
-			UnmergedPathException {
+			UnmergedPathException, JGitInternalException,
+			WrongRepositoryStateException {
 		Git git = new Git(db);
 		CommitCommand commitCmd = git.commit();
 		commitCmd.setMessage("initial commit").call();
@@ -114,4 +124,31 @@
 		} catch (IllegalStateException e) {
 		}
 	}
+
+	public void testMergeEmptyBranches() throws IOException, NoHeadException,
+			NoMessageException, ConcurrentRefUpdateException,
+			JGitInternalException, WrongRepositoryStateException {
+		Git git = new Git(db);
+		git.commit().setMessage("initial commit").call();
+		RefUpdate r = db.updateRef("refs/heads/side");
+		r.setNewObjectId(db.resolve(Constants.HEAD));
+		assertEquals(r.forceUpdate(), RefUpdate.Result.NEW);
+		RevCommit second = git.commit().setMessage("second commit").setCommitter(committer).call();
+		db.updateRef(Constants.HEAD).link("refs/heads/side");
+		RevCommit firstSide = git.commit().setMessage("first side commit").setAuthor(author).call();
+
+		FileWriter wr = new FileWriter(new File(db.getDirectory(),
+				Constants.MERGE_HEAD));
+		wr.write(ObjectId.toString(db.resolve("refs/heads/master")));
+		wr.close();
+		wr = new FileWriter(new File(db.getDirectory(), Constants.MERGE_MSG));
+		wr.write("merging");
+		wr.close();
+
+		RevCommit commit = git.commit().call();
+		RevCommit[] parents = commit.getParents();
+		assertEquals(parents[0], firstSide);
+		assertEquals(parents[1], second);
+		assertTrue(parents.length==2);
+	}
 }
diff --git a/org.eclipse.jgit/resources/org/eclipse/jgit/JGitText.properties b/org.eclipse.jgit/resources/org/eclipse/jgit/JGitText.properties
index 4cdf914..e9ed28a 100644
--- a/org.eclipse.jgit/resources/org/eclipse/jgit/JGitText.properties
+++ b/org.eclipse.jgit/resources/org/eclipse/jgit/JGitText.properties
@@ -27,6 +27,7 @@
 blobNotFoundForPath=Blob not found: {0} for path: {1}
 cannotBeCombined=Cannot be combined.
 cannotCombineTreeFilterWithRevFilter=Cannot combine TreeFilter {0} with RefFilter {1}.
+cannotCommitOnARepoWithState=Cannot commit on a repo with state: {0}
 cannotCommitWriteTo=Cannot commit write to {0}
 cannotConnectPipes=cannot connect pipes
 cannotConvertScriptToText=Cannot convert script to text
@@ -137,6 +138,7 @@
 errorReadingInfoRefs=error reading info/refs
 exceptionCaughtDuringExecutionOfCommitCommand=Exception caught during execution of commit command
 exceptionOccuredDuringAddingOfOptionToALogCommand=Exception occured during adding of {0} as option to a Log command
+exceptionOccuredDuringReadingOfGIT_DIR=Exception occured during reading of $GIT_DIR/{0}. {1}
 expectedACKNAKFoundEOF=Expected ACK/NAK, found EOF
 expectedACKNAKGot=Expected ACK/NAK, got: {0}
 expectedBooleanStringValue=Expected boolean string value
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/JGitText.java b/org.eclipse.jgit/src/org/eclipse/jgit/JGitText.java
index fbc17aa..a7c2e68 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/JGitText.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/JGitText.java
@@ -87,6 +87,7 @@
 	/***/ public String blobNotFoundForPath;
 	/***/ public String cannotBeCombined;
 	/***/ public String cannotCombineTreeFilterWithRevFilter;
+	/***/ public String cannotCommitOnARepoWithState;
 	/***/ public String cannotCommitWriteTo;
 	/***/ public String cannotConnectPipes;
 	/***/ public String cannotConvertScriptToText;
@@ -197,6 +198,7 @@
 	/***/ public String errorReadingInfoRefs;
 	/***/ public String exceptionCaughtDuringExecutionOfCommitCommand;
 	/***/ public String exceptionOccuredDuringAddingOfOptionToALogCommand;
+	/***/ public String exceptionOccuredDuringReadingOfGIT_DIR;
 	/***/ public String expectedACKNAKFoundEOF;
 	/***/ public String expectedACKNAKGot;
 	/***/ public String expectedBooleanStringValue;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
index 542c821..eef952e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
@@ -42,8 +42,11 @@
  */
 package org.eclipse.jgit.api;
 
+import java.io.File;
 import java.io.IOException;
 import java.text.MessageFormat;
+import java.util.LinkedList;
+import java.util.List;
 
 import org.eclipse.jgit.JGitText;
 import org.eclipse.jgit.dircache.DirCache;
@@ -57,6 +60,7 @@
 import org.eclipse.jgit.lib.RefUpdate;
 import org.eclipse.jgit.lib.RefUpdate.Result;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.RepositoryState;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevWalk;
 
@@ -77,6 +81,12 @@
 	private String message;
 
 	/**
+	 * parents this commit should have. The current HEAD will be in this list
+	 * and also all commits mentioned in .git/MERGE_HEAD
+	 */
+	private List<ObjectId> parents = new LinkedList<ObjectId>();
+
+	/**
 	 * @param repo
 	 */
 	protected CommitCommand(Repository repo) {
@@ -96,6 +106,8 @@
 	 *             when called without specifying a commit message
 	 * @throws UnmergedPathException
 	 *             when the current index contained unmerged pathes (conflicts)
+	 * @throws WrongRepositoryStateException
+	 *             when repository is not in the right state for committing
 	 * @throws JGitInternalException
 	 *             a low-level exception of JGit has occurred. The original
 	 *             exception can be retrieved by calling
@@ -106,9 +118,14 @@
 	 */
 	public RevCommit call() throws NoHeadException, NoMessageException,
 			UnmergedPathException, ConcurrentRefUpdateException,
-			JGitInternalException {
+			JGitInternalException, WrongRepositoryStateException {
 		checkCallable();
-		processOptions();
+
+		RepositoryState state = repo.getRepositoryState();
+		if (!state.canCommit())
+			throw new WrongRepositoryStateException(MessageFormat.format(
+					JGitText.get().cannotCommitOnARepoWithState, state.name()));
+		processOptions(state);
 
 		try {
 			Ref head = repo.getRef(Constants.HEAD);
@@ -117,7 +134,9 @@
 						JGitText.get().commitOnRepoWithoutHEADCurrentlyNotSupported);
 
 			// determine the current HEAD and the commit it is referring to
-			ObjectId parentID = repo.resolve(Constants.HEAD + "^{commit}");
+			ObjectId headId = repo.resolve(Constants.HEAD + "^{commit}");
+			if (headId != null)
+				parents.add(0, headId);
 
 			// lock the index
 			DirCache index = DirCache.lock(repo);
@@ -134,8 +153,8 @@
 				commit.setCommitter(committer);
 				commit.setAuthor(author);
 				commit.setMessage(message);
-				if (parentID != null)
-					commit.setParentIds(new ObjectId[] { parentID });
+
+				commit.setParentIds(parents.toArray(new ObjectId[]{}));
 				commit.setTreeId(indexTreeId);
 				ObjectId commitId = repoWriter.writeCommit(commit);
 
@@ -145,12 +164,20 @@
 				ru.setRefLogMessage("commit : " + revCommit.getShortMessage(),
 						false);
 
-				ru.setExpectedOldObjectId(parentID);
+				ru.setExpectedOldObjectId(headId);
 				Result rc = ru.update();
 				switch (rc) {
 				case NEW:
 				case FAST_FORWARD:
 					setCallable(false);
+					if (state == RepositoryState.MERGING_RESOLVED) {
+						// Commit was successful. Now delete the files
+						// used for merge commits
+						new File(repo.getDirectory(), Constants.MERGE_HEAD)
+								.delete();
+						new File(repo.getDirectory(), Constants.MERGE_MSG)
+								.delete();
+					}
 					return revCommit;
 				case REJECTED:
 				case LOCK_FAILURE:
@@ -179,18 +206,41 @@
 	 * Sets default values for not explicitly specified options. Then validates
 	 * that all required data has been provided.
 	 *
+	 * @param state
+	 *            the state of the repository we are working on
+	 *
 	 * @throws NoMessageException
 	 *             if the commit message has not been specified
 	 */
-	private void processOptions() throws NoMessageException {
-		if (message == null)
-			// as long as we don't suppport -C option we have to have
-			// an explicit message
-			throw new NoMessageException(JGitText.get().commitMessageNotSpecified);
+	private void processOptions(RepositoryState state) throws NoMessageException {
 		if (committer == null)
 			committer = new PersonIdent(repo);
 		if (author == null)
 			author = committer;
+
+		// when doing a merge commit parse MERGE_HEAD and MERGE_MSG files
+		if (state == RepositoryState.MERGING_RESOLVED) {
+			try {
+				parents = repo.readMergeHeads();
+			} catch (IOException e) {
+				throw new JGitInternalException(MessageFormat.format(
+						JGitText.get().exceptionOccuredDuringReadingOfGIT_DIR,
+						Constants.MERGE_HEAD, e));
+			}
+			if (message == null) {
+				try {
+					message = repo.readMergeCommitMsg();
+				} catch (IOException e) {
+					throw new JGitInternalException(MessageFormat.format(
+							JGitText.get().exceptionOccuredDuringReadingOfGIT_DIR,
+							Constants.MERGE_MSG, e));
+				}
+			}
+		}
+		if (message == null)
+			// as long as we don't suppport -C option we have to have
+			// an explicit message
+			throw new NoMessageException(JGitText.get().commitMessageNotSpecified);
 	}
 
 	/**
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/WrongRepositoryStateException.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/WrongRepositoryStateException.java
new file mode 100644
index 0000000..833cf8d
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/WrongRepositoryStateException.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright (C) 2010, Christian Halstrick <christian.halstrick@sap.com> and
+ * other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Distribution License v1.0 which accompanies this
+ * distribution, is reproduced below, and is available at
+ * http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the names of its
+ * contributors may be used to endorse or promote products derived from this
+ * software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.api;
+
+/**
+ * Exception thrown when the state of the repository doesn't allow the execution
+ * of a certain command. E.g. when a CommitCommand should be executed on a
+ * repository with unresolved conflicts this exception will be thrown.
+ */
+public class WrongRepositoryStateException extends GitAPIException {
+	private static final long serialVersionUID = 1L;
+
+	WrongRepositoryStateException(String message, Throwable cause) {
+		super(message, cause);
+	}
+
+	WrongRepositoryStateException(String message) {
+		super(message);
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java
index 37836f3..03ab629 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Constants.java
@@ -518,6 +518,12 @@
 		CHARSET = Charset.forName(CHARACTER_ENCODING);
 	}
 
+	/** name of the file containing the commit msg for a merge commit */
+	public static final String MERGE_MSG = "MERGE_MSG";
+
+	/** name of the file containing the IDs of the parents of a merge commit */
+	public static final String MERGE_HEAD = "MERGE_HEAD";
+
 	private Constants() {
 		// Hide the default constructor
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
index e4d857b..233cecf 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
@@ -47,6 +47,7 @@
 package org.eclipse.jgit.lib;
 
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.text.MessageFormat;
 import java.util.ArrayList;
@@ -61,12 +62,14 @@
 import java.util.Vector;
 import java.util.concurrent.atomic.AtomicInteger;
 
-import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.JGitText;
+import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.errors.RevisionSyntaxException;
 import org.eclipse.jgit.util.FS;
+import org.eclipse.jgit.util.IO;
+import org.eclipse.jgit.util.RawParseUtils;
 import org.eclipse.jgit.util.SystemReader;
 
 /**
@@ -1338,4 +1341,55 @@
 			return new ReflogReader(this, ref.getName());
 		return null;
 	}
+
+	/**
+	 * Return the information stored in the file $GIT_DIR/MERGE_MSG. In this
+	 * file operations triggering a merge will store a template for the commit
+	 * message of the merge commit.
+	 *
+	 * @return a String containing the content of the MERGE_MSG file or
+	 *         {@code null} if this file doesn't exist
+	 * @throws IOException
+	 */
+	public String readMergeCommitMsg() throws IOException {
+		File mergeMsgFile = new File(gitDir, Constants.MERGE_MSG);
+		try {
+			return new String(IO.readFully(mergeMsgFile));
+		} catch (FileNotFoundException e) {
+			// MERGE_MSG file has disappeared in the meantime
+			// ignore it
+			return null;
+		}
+	}
+
+	/**
+	 * Return the information stored in the file $GIT_DIR/MERGE_HEAD. In this
+	 * file operations triggering a merge will store the IDs of all heads which
+	 * should be merged together with HEAD.
+	 *
+	 * @return a list of {@link Commit}s which IDs are listed in the MERGE_HEAD
+	 *         file or {@code null} if this file doesn't exist. Also if the file
+	 *         exists but is empty {@code null} will be returned
+	 * @throws IOException
+	 */
+	public List<ObjectId> readMergeHeads() throws IOException {
+		File mergeHeadFile = new File(gitDir, Constants.MERGE_HEAD);
+		byte[] raw;
+		try {
+			raw = IO.readFully(mergeHeadFile);
+		} catch (FileNotFoundException notFound) {
+			return new LinkedList<ObjectId>();
+		}
+
+		if (raw.length == 0)
+			throw new IOException("MERGE_HEAD file empty: " + mergeHeadFile);
+
+		LinkedList<ObjectId> heads = new LinkedList<ObjectId>();
+		for (int p = 0; p < raw.length;) {
+			heads.add(ObjectId.fromString(raw, p));
+			p = RawParseUtils
+					.nextLF(raw, p + Constants.OBJECT_ID_STRING_LENGTH);
+		}
+		return heads;
+	}
 }