Index: lib/Transforms/Utils/CloneFunction.cpp
===================================================================
--- lib/Transforms/Utils/CloneFunction.cpp
+++ lib/Transforms/Utils/CloneFunction.cpp
@@ -684,6 +684,22 @@
                        RF_NoModuleLevelChanges | RF_IgnoreMissingLocals);
 }
 
+/// \brief Clones the original loop \p OrigLoop structure
+/// and keeps it ready to add the basic blocks.
+static void createNewLoops(Loop *OrigLoop, LoopInfo *LI, Loop *ParentLoop,
+   std::map<Loop*, Loop*>  &ClonedLoopMap) {
+  if (OrigLoop->empty()) return;
+
+  for (auto CurrLoop :  OrigLoop->getSubLoops()) {
+    Loop *NewLoop = new Loop();
+    ParentLoop->addChildLoop(NewLoop);
+    ClonedLoopMap[CurrLoop] = NewLoop;
+
+    // Recursively add the new loops.
+    createNewLoops(CurrLoop, LI, NewLoop, ClonedLoopMap);
+  }
+}
+
 /// \brief Clones a loop \p OrigLoop.  Returns the loop and the blocks in \p
 /// Blocks.
 ///
@@ -694,8 +710,6 @@
                                    const Twine &NameSuffix, LoopInfo *LI,
                                    DominatorTree *DT,
                                    SmallVectorImpl<BasicBlock *> &Blocks) {
-  assert(OrigLoop->getSubLoops().empty() && 
-         "Loop to be cloned cannot have inner loop");
   Function *F = OrigLoop->getHeader()->getParent();
   Loop *ParentLoop = OrigLoop->getParentLoop();
 
@@ -705,6 +719,14 @@
   else
     LI->addTopLevelLoop(NewLoop);
 
+  // Map each old Loop with new one.
+  std::map<Loop*, Loop*> ClonedLoopMap;
+  // Add the top level loop provided for cloning.
+  ClonedLoopMap[OrigLoop] = NewLoop;
+
+  // Recursively clone the loop structure.
+  createNewLoops(OrigLoop, LI, NewLoop, ClonedLoopMap);
+
   BasicBlock *OrigPH = OrigLoop->getLoopPreheader();
   assert(OrigPH && "No preheader");
   BasicBlock *NewPH = CloneBasicBlock(OrigPH, VMap, NameSuffix, F);
@@ -723,8 +745,13 @@
     BasicBlock *NewBB = CloneBasicBlock(BB, VMap, NameSuffix, F);
     VMap[BB] = NewBB;
 
+    // Get the innermost loop for the BB.
+    Loop* L = LI->getLoopFor(BB);
+    // Get the corresponding cloned loop.
+    Loop* NewClonedLoop = ClonedLoopMap[L];
+    assert(NewClonedLoop && "Could not find the corresponding cloned loop");
     // Update LoopInfo.
-    NewLoop->addBasicBlockToLoop(NewBB, *LI);
+    NewClonedLoop->addBasicBlockToLoop(NewBB, *LI);
 
     // Add DominatorTree node. After seeing all blocks, update to correct IDom.
     DT->addNewBlock(NewBB, NewPH);