diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java
index 045300613..17ccb9726 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/SimilarityIndex.java
@@ -76,6 +76,9 @@ class SimilarityIndex {
 	 */
 	private static final int KEY_SHIFT = 32;
 
+	/** Maximum value of the count field, also mask to extract the count. */
+	private static final long MAX_COUNT = (1L << KEY_SHIFT) - 1;
+
 	/** Total size of the file we hashed into the structure. */
 	private long fileSize;
 
@@ -196,11 +199,11 @@ class SimilarityIndex {
 		return (int) ((common(dst) * maxScore) / max);
 	}
 
-	int common(SimilarityIndex dst) {
+	long common(SimilarityIndex dst) {
 		return common(this, dst);
 	}
 
-	private static int common(SimilarityIndex src, SimilarityIndex dst) {
+	private static long common(SimilarityIndex src, SimilarityIndex dst) {
 		int srcIdx = src.packedIndex(0);
 		int dstIdx = dst.packedIndex(0);
 		long[] srcHash = src.idHash;
@@ -208,12 +211,12 @@ class SimilarityIndex {
 		return common(srcHash, srcIdx, dstHash, dstIdx);
 	}
 
-	private static int common(long[] srcHash, int srcIdx, //
+	private static long common(long[] srcHash, int srcIdx, //
 			long[] dstHash, int dstIdx) {
 		if (srcIdx == srcHash.length || dstIdx == dstHash.length)
 			return 0;
 
-		int common = 0;
+		long common = 0;
 		int srcKey = keyOf(srcHash[srcIdx]);
 		int dstKey = keyOf(dstHash[dstIdx]);
 
@@ -287,13 +290,15 @@ class SimilarityIndex {
 					j = slot(key);
 					continue;
 				}
-				idHash[j] = (((long) key) << KEY_SHIFT) | cnt;
+				idHash[j] = pair(key, cnt);
 				idSize++;
 				return;
 
 			} else if (keyOf(v) == key) {
-				// Same key, increment the counter.
-				idHash[j] = v + cnt;
+				// Same key, increment the counter. If it overflows, fail
+				// indexing to prevent the key from being impacted.
+				//
+				idHash[j] = pair(key, countOf(v) + cnt);
 				return;
 
 			} else if (++j >= idHash.length) {
@@ -302,6 +307,12 @@ class SimilarityIndex {
 		}
 	}
 
+	private static long pair(int key, long cnt) throws TableFullException {
+		if (MAX_COUNT < cnt)
+			throw new TableFullException();
+		return (((long) key) << KEY_SHIFT) | cnt;
+	}
+
 	private int slot(int key) {
 		// We use 31 - idHashBits because the upper bit was already forced
 		// to be 0 and we want the remaining high bits to be used as the
@@ -346,8 +357,8 @@ class SimilarityIndex {
 		return (int) (v >>> KEY_SHIFT);
 	}
 
-	private static int countOf(long v) {
-		return (int) v;
+	private static long countOf(long v) {
+		return v & MAX_COUNT;
 	}
 
 	static class TableFullException extends Exception {