diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
index 244438a59..2bf75b035 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
@@ -25,6 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.reads;
 
 import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
 import java.io.FileInputStream;
@@ -349,7 +350,18 @@ public class GATKBAMIndex {
 
     private void read(final ByteBuffer buffer) {
         try {
-            fileChannel.read(buffer);
+            int bytesExpected = buffer.limit();
+            int bytesRead = fileChannel.read(buffer);
+
+            // We have a rigid expectation here to read in exactly the number of bytes we've limited
+            // our buffer to -- if we read in fewer bytes than this, or encounter EOF (-1), the index
+            // must be truncated or otherwise corrupt:
+            if ( bytesRead < bytesExpected ) {
+                throw new UserException.MalformedFile(mFile, String.format("Premature end-of-file while reading BAM index file %s. " +
+                                                                           "It's likely that this file is truncated or corrupt -- " +
+                                                                           "Please try re-indexing the corresponding BAM file.",
+                                                                           mFile));
+            }
         }
         catch(IOException ex) {
             throw new ReviewedStingException("Index: unable to read bytes from index file " + mFile);
diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java
index fde0ce62f..8cf9f7ce0 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java
@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.datasources.reads;
 import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMSequenceDictionary;
 import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -91,4 +92,16 @@ public class GATKBAMIndexUnitTest extends BaseTest {
         Assert.assertEquals(bamIndex.getLevelSize(5),37448-4681+1);
     }
 
+    @Test( expectedExceptions = UserException.MalformedFile.class )
+    public void testDetectTruncatedBamIndexWordBoundary() {
+        GATKBAMIndex index = new GATKBAMIndex(new File(validationDataLocation + "truncated_at_word_boundary.bai"));
+        index.readReferenceSequence(0);
+    }
+
+    @Test( expectedExceptions = UserException.MalformedFile.class )
+    public void testDetectTruncatedBamIndexNonWordBoundary() {
+        GATKBAMIndex index = new GATKBAMIndex(new File(validationDataLocation + "truncated_at_non_word_boundary.bai"));
+        index.readReferenceSequence(0);
+    }
+
 }