diff --git a/src/core.cpp b/src/core.cpp
index e52327ba8e..85cca1ebf0 100644
--- a/src/core.cpp
+++ b/src/core.cpp
@@ -224,29 +224,66 @@ uint256 CBlockHeader::GetHash() const
     return Hash(BEGIN(nVersion), END(nNonce));
 }
 
-uint256 CBlock::BuildMerkleTree() const
+uint256 CBlock::BuildMerkleTree(bool* fMutated) const
 {
-    // WARNING! If you're reading this because you're learning about crypto
-    // and/or designing a new system that will use merkle trees, keep in mind
-    // that the following merkle tree algorithm has a serious flaw related to
-    // duplicate txids, resulting in a vulnerability. (CVE-2012-2459) Bitcoin
-    // has since worked around the flaw, but for new applications you should
-    // use something different; don't just copy-and-paste this code without
-    // understanding the problem first.
+    /* WARNING! If you're reading this because you're learning about crypto
+       and/or designing a new system that will use merkle trees, keep in mind
+       that the following merkle tree algorithm has a serious flaw related to
+       duplicate txids, resulting in a vulnerability (CVE-2012-2459).
+
+       The reason is that if the number of hashes in the list at a given time
+       is odd, the last one is duplicated before computing the next level (which
+       is unusual in Merkle trees). This results in certain sequences of
+       transactions leading to the same merkle root. For example, these two
+       trees:
+
+                    A               A
+                  /  \            /   \
+                B     C         B       C
+               / \    |        / \     / \
+              D   E   F       D   E   F   F
+             / \ / \ / \     / \ / \ / \ / \
+             1 2 3 4 5 6     1 2 3 4 5 6 5 6
+
+       for transaction lists [1,2,3,4,5,6] and [1,2,3,4,5,6,5,6] (where 5 and
+       6 are repeated) result in the same root hash A (because the hash of both
+       of (F) and (F,F) is C).
+
+       The vulnerability results from being able to send a block with such a
+       transaction list, with the same merkle root, and the same block hash as
+       the original without duplication, resulting in failed validation. If the
+       receiving node proceeds to mark that block as permanently invalid
+       however, it will fail to accept further unmodified (and thus potentially
+       valid) versions of the same block. We defend against this by detecting
+       the case where we would hash two identical hashes at the end of the list
+       together, and treating that identically to the block having an invalid
+       merkle root. Assuming no double-SHA256 collisions, this will detect all
+       known ways of changing the transactions without affecting the merkle
+       root.
+    */
     vMerkleTree.clear();
+    vMerkleTree.reserve(vtx.size() * 2 + 16); // Safe upper bound for the number of total nodes.
     BOOST_FOREACH(const CTransaction& tx, vtx)
         vMerkleTree.push_back(tx.GetHash());
     int j = 0;
+    bool mutated = false;
     for (int nSize = vtx.size(); nSize > 1; nSize = (nSize + 1) / 2)
     {
         for (int i = 0; i < nSize; i += 2)
         {
             int i2 = std::min(i+1, nSize-1);
+            if (i2 == i + 1 && i2 + 1 == nSize && vMerkleTree[j+i] == vMerkleTree[j+i2]) {
+                // Two identical hashes at the end of the list at a particular level.
+                mutated = true;
+            }
             vMerkleTree.push_back(Hash(BEGIN(vMerkleTree[j+i]),  END(vMerkleTree[j+i]),
                                        BEGIN(vMerkleTree[j+i2]), END(vMerkleTree[j+i2])));
         }
         j += nSize;
     }
+    if (fMutated) {
+        *fMutated = mutated;
+    }
     return (vMerkleTree.empty() ? 0 : vMerkleTree.back());
 }
 
diff --git a/src/core.h b/src/core.h
index 9a2ac47487..de41b8621b 100644
--- a/src/core.h
+++ b/src/core.h
@@ -528,7 +528,11 @@ public:
         return block;
     }
 
-    uint256 BuildMerkleTree() const;
+    // Build the in-memory merkle tree for this block and return the merkle root.
+    // If non-NULL, *mutated is set to whether mutation was detected in the merkle
+    // tree (a duplication of transactions in the block leading to an identical
+    // merkle root).
+    uint256 BuildMerkleTree(bool* mutated = NULL) const;
 
     std::vector<uint256> GetMerkleBranch(int nIndex) const;
     static uint256 CheckMerkleBranch(uint256 hash, const std::vector<uint256>& vMerkleBranch, int nIndex);
diff --git a/src/main.cpp b/src/main.cpp
index 15c3916a6f..d79644e638 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -2289,13 +2289,12 @@ bool CheckBlock(const CBlock& block, CValidationState& state, bool fCheckPOW, bo
         if (!CheckTransaction(tx, state))
             return error("CheckBlock() : CheckTransaction failed");
 
-    // Check for duplicate txids. This is caught by ConnectInputs(),
-    // but catching it earlier avoids a potential DoS attack:
-    set<uint256> uniqueTx;
-    BOOST_FOREACH(const CTransaction &tx, block.vtx) {
-        uniqueTx.insert(tx.GetHash());
-    }
-    if (uniqueTx.size() != block.vtx.size())
+    // Check for merkle tree malleability (CVE-2012-2459): repeating sequences
+    // of transactions in a block without affecting the merkle root of a block,
+    // while still invalidating it.
+    bool mutated;
+    uint256 hashMerkleRoot2 = block.BuildMerkleTree(&mutated);
+    if (mutated)
         return state.DoS(100, error("CheckBlock() : duplicate transaction"),
                          REJECT_INVALID, "bad-txns-duplicate", true);
 
@@ -2309,7 +2308,7 @@ bool CheckBlock(const CBlock& block, CValidationState& state, bool fCheckPOW, bo
                          REJECT_INVALID, "bad-blk-sigops", true);
 
     // Check merkle root
-    if (fCheckMerkleRoot && block.hashMerkleRoot != block.BuildMerkleTree())
+    if (fCheckMerkleRoot && block.hashMerkleRoot != hashMerkleRoot2)
         return state.DoS(100, error("CheckBlock() : hashMerkleRoot mismatch"),
                          REJECT_INVALID, "bad-txnmrklroot", true);