Index: lib/Transforms/IPO/SampleProfile.cpp
===================================================================
--- lib/Transforms/IPO/SampleProfile.cpp
+++ lib/Transforms/IPO/SampleProfile.cpp
@@ -1162,9 +1162,13 @@
       }
     }
 
+    uint64_t TempWeight;
     // Only set weights if there is at least one non-zero weight.
     // In any other case, let the analyzer set weights.
-    if (MaxWeight > 0) {
+    // Do not set weights if the weights are present. In ThinLTO, the profile
+    // annotation is done twice. If the first annotation already set the
+    // weights, the second pass does not need to set it.
+    if (MaxWeight > 0 && !TI->extractProfTotalWeight(TempWeight)) {
       DEBUG(dbgs() << "SUCCESS. Found non-zero weights.\n");
       TI->setMetadata(llvm::LLVMContext::MD_prof,
                       MDB.createBranchWeights(Weights));
Index: test/Transforms/SampleProfile/branch.ll
===================================================================
--- test/Transforms/SampleProfile/branch.ll
+++ test/Transforms/SampleProfile/branch.ll
@@ -87,7 +87,9 @@
   %6 = load i32, i32* %u, align 4, !dbg !46
   %7 = load i32, i32* %limit, align 4, !dbg !48
   %cmp5 = icmp slt i32 %6, %7, !dbg !49
-  br i1 %cmp5, label %for.body, label %for.end, !dbg !50
+  br i1 %cmp5, label %for.body, label %for.end, !dbg !50, !prof !80
+; CHECK: edge for.cond -> for.body probability is 0x73333333 / 0x80000000 = 90.00%
+; CHECK: edge for.cond -> for.end probability is 0x0ccccccd / 0x80000000 = 10.00%
 
 for.body:                                         ; preds = %for.cond
   call void @llvm.dbg.declare(metadata double* %x, metadata !51, metadata !17), !dbg !53
@@ -237,3 +239,4 @@
 !77 = !DILocation(line: 20, column: 4, scope: !6)
 !78 = !DILocation(line: 21, column: 4, scope: !6)
 !79 = !DILocation(line: 22, column: 2, scope: !6)
+!80 = !{!"branch_weights", i32 90, i32 10}