diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index c924001b1..239b9ad1a 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -306,7 +306,8 @@ public class GenomeAnalysisEngine {
     }
 
     /**
-     * Verifies that the supplied set of reads files mesh with what the walker says it requires.
+     * Verifies that the supplied set of reads files mesh with what the walker says it requires,
+     * and also makes sure that there were no duplicate SAM files specified on the command line.
      */
     protected void validateSuppliedReads() {
         GATKArgumentCollection arguments = this.getArguments();
@@ -317,6 +318,32 @@ public class GenomeAnalysisEngine {
         // Check what the walker says is allowed against what was provided on the command line.
         if ((arguments.samFiles != null && arguments.samFiles.size() > 0) && !WalkerManager.isAllowed(walker, DataSource.READS))
             throw new ArgumentException("Walker does not allow reads but reads were provided.");
+
+        // Make sure no SAM files were specified multiple times by the user.
+        checkForDuplicateSamFiles();
+    }
+
+    /**
+     * Checks whether there are SAM files that appear multiple times in the fully unpacked list of
+     * SAM files (samReaderIDs). If there are, throws an ArgumentException listing the files in question.
+     */
+    protected void checkForDuplicateSamFiles() {
+        Set<SAMReaderID> encounteredSamFiles = new HashSet<SAMReaderID>();
+        Set<String> duplicateSamFiles = new LinkedHashSet<String>();
+
+        for ( SAMReaderID samFile : samReaderIDs ) {
+            if ( encounteredSamFiles.contains(samFile) ) {
+                duplicateSamFiles.add(samFile.getSamFilePath());
+            }
+            else {
+                encounteredSamFiles.add(samFile);
+            }
+        }
+
+        if ( duplicateSamFiles.size() > 0 ) {
+            throw new ArgumentException("The following BAM files appear multiple times in the list of input files: " +
+                                        duplicateSamFiles + " BAM files may be specified at most once.");
+        }
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java
index 3eee05a54..c84db7770 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java
@@ -41,6 +41,19 @@ public class SAMReaderID implements Comparable {
         this(new File(samFileName),tags);        
     }
 
+    /**
+     * Gets the absolute pathname of this SAM file
+     * @return  The absolute pathname of this reader's SAM file,
+     *          or null if this reader has no associated SAM file
+     */
+    public String getSamFilePath() {
+        if ( samFile == null ) {
+            return null;
+        }
+
+        return samFile.getAbsolutePath();
+    }
+
     /**
      * Gets the tags associated with the given BAM file.
      * @return A collection of the tags associated with this file.
diff --git a/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java b/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
new file mode 100644
index 000000000..30bf2db07
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
@@ -0,0 +1,69 @@
+/*
+ * Copyright (c) 2010, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk;
+
+import org.testng.annotations.Test;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.commandline.ArgumentException;
+import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
+import org.broadinstitute.sting.commandline.Tags;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Collection;
+
+
+/**
+ * Tests selected functionality in the GenomeAnalysisEngine class
+ */
+public class GenomeAnalysisEngineUnitTest extends BaseTest {
+
+    @Test(expectedExceptions=ArgumentException.class)
+    public void testDuplicateSamFileHandlingSingleDuplicate() throws Exception {
+        GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
+
+        Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
+        samFiles.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags()));
+        samFiles.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags()));
+
+        testEngine.setSAMFileIDs(samFiles);
+        testEngine.checkForDuplicateSamFiles();
+    }
+
+    @Test(expectedExceptions=ArgumentException.class)
+    public void testDuplicateSamFileHandlingMultipleDuplicates() throws Exception {
+        GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
+
+        Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
+        samFiles.add(new SAMReaderID(new File("testdata/exampleBAM.bam"),  new Tags()));
+        samFiles.add(new SAMReaderID(new File("testdata/exampleNORG.bam"), new Tags()));
+        samFiles.add(new SAMReaderID(new File("testdata/exampleBAM.bam"),  new Tags()));
+        samFiles.add(new SAMReaderID(new File("testdata/exampleNORG.bam"), new Tags()));
+
+        testEngine.setSAMFileIDs(samFiles);
+        testEngine.checkForDuplicateSamFiles();
+    }
+}