diff --git a/mlir/test/mlir-cpu-runner/lit.local.cfg b/mlir/test/mlir-cpu-runner/lit.local.cfg
--- a/mlir/test/mlir-cpu-runner/lit.local.cfg
+++ b/mlir/test/mlir-cpu-runner/lit.local.cfg
@@ -4,6 +4,10 @@
 if sys.platform == 'win32':
     config.unsupported = True
 
+# MSAN does not work with JIT.
+if 'msan' in config.available_features:
+  config.unsupported = True
+
 # Requires the native target to be configured in.
 if 'llvm_has_native_target' not in config.available_features:
     config.unsupported = True
diff --git a/mlir/unittests/ExecutionEngine/Invoke.cpp b/mlir/unittests/ExecutionEngine/Invoke.cpp
--- a/mlir/unittests/ExecutionEngine/Invoke.cpp
+++ b/mlir/unittests/ExecutionEngine/Invoke.cpp
@@ -232,7 +232,13 @@
     elt *= coefficient;
 }
 
-TEST(NativeMemRefJit, JITCallback) {
+// MSAN does not work with JIT.
+#if __has_feature(memory_sanitizer)
+#define MAYBE_JITCallback DISABLED_JITCallback
+#else
+#define MAYBE_JITCallback JITCallback
+#endif
+TEST(NativeMemRefJit, MAYBE_JITCallback) {
   constexpr int k = 2;
   constexpr int m = 2;
   int64_t shape[] = {k, m};