diff --git a/src/dawn/native/d3d/ShaderUtils.cpp b/src/dawn/native/d3d/ShaderUtils.cpp
index 222dc34374..a0e13d47cb 100644
--- a/src/dawn/native/d3d/ShaderUtils.cpp
+++ b/src/dawn/native/d3d/ShaderUtils.cpp
@@ -232,6 +232,7 @@ ResultOrError<std::string> TranslateToHLSL(
         // Pass in the actually used interstage locations for tint to potentially truncate unused
         // outputs.
         options.interstage_locations = r.interstageLocations;
+        options.truncate_interstage_variables = true;
     }
 
     options.polyfill_reflect_vec2_f32 = r.polyfillReflectVec2F32;
diff --git a/src/dawn/tests/end2end/ShaderTests.cpp b/src/dawn/tests/end2end/ShaderTests.cpp
index 2e91325bfc..b81f4eed32 100644
--- a/src/dawn/tests/end2end/ShaderTests.cpp
+++ b/src/dawn/tests/end2end/ShaderTests.cpp
@@ -549,6 +549,42 @@ fn fragmentMain() -> @location(0) vec4f {
     wgpu::RenderPipeline pipeline = device.CreateRenderPipeline(&rpDesc);
 }
 
+// Regression test for crbug.com/dawn/1733. Even when user defined attribute input is empty,
+// Builtin input for the next stage could still cause register mismatch issue on D3D12 HLSL
+// compiler. So the TruncateInterstageVariables transform should still be run. This test is not in
+// dawn_unittests/RenderPipelineValidationTests because we want to test the compilation of the
+// pipeline in D3D12 backend.
+TEST_P(ShaderTests, WGSLInterstageVariablesEmptyUserAttributeSubset) {
+    std::string shader = R"(
+struct VertexOut {
+    @builtin(position) position : vec4f,
+    @location(1) attribute1 : f32,
+    @location(3) attribute3 : vec4f,
+}
+
+@vertex
+fn vertexMain() -> VertexOut {
+    var output : VertexOut;
+    output.position = vec4f(0.0, 0.0, 0.0, 1.0);
+    output.attribute1 = 1.0;
+    output.attribute3 = vec4f(0.0, 0.0, 0.0, 1.0);
+    return output;
+}
+
+@fragment
+fn fragmentMain(@builtin(position) position : vec4<f32>) -> @location(0) vec4f {
+    return vec4f(0.0, 0.0, 0.0, 1.0);
+})";
+    wgpu::ShaderModule shaderModule = utils::CreateShaderModule(device, shader.c_str());
+
+    utils::ComboRenderPipelineDescriptor rpDesc;
+    rpDesc.vertex.module = shaderModule;
+    rpDesc.vertex.entryPoint = "vertexMain";
+    rpDesc.cFragment.module = shaderModule;
+    rpDesc.cFragment.entryPoint = "fragmentMain";
+    wgpu::RenderPipeline pipeline = device.CreateRenderPipeline(&rpDesc);
+}
+
 // This is a regression test for an issue caused by the FirstIndexOffset transfrom being done before
 // the BindingRemapper, causing an intermediate AST to be invalid (and fail the overall
 // compilation).
diff --git a/src/tint/writer/hlsl/generator.h b/src/tint/writer/hlsl/generator.h
index 9b79ad1887..804b449cb4 100644
--- a/src/tint/writer/hlsl/generator.h
+++ b/src/tint/writer/hlsl/generator.h
@@ -74,6 +74,9 @@ struct Options {
     /// This is potentially used for truncating unused interstage outputs at current shader stage.
     std::bitset<16> interstage_locations;
 
+    /// Set to `true` to run the TruncateInterstageVariables transform.
+    bool truncate_interstage_variables = false;
+
     /// Set to `true` to generate polyfill for `reflect` builtin for vec2<f32>
     bool polyfill_reflect_vec2_f32 = false;
 
diff --git a/src/tint/writer/hlsl/generator_impl.cc b/src/tint/writer/hlsl/generator_impl.cc
index 4d07b4ff31..5e4ae33f94 100644
--- a/src/tint/writer/hlsl/generator_impl.cc
+++ b/src/tint/writer/hlsl/generator_impl.cc
@@ -241,13 +241,11 @@ SanitizedResult Sanitize(const Program* in, const Options& options) {
     // CanonicalizeEntryPointIO must come after Robustness
     manager.Add<transform::CanonicalizeEntryPointIO>();
 
-    if (options.interstage_locations.any()) {
+    if (options.truncate_interstage_variables) {
         // When interstage_locations is empty, it means there's no user-defined interstage variables
-        // being used in the next stage. This is treated as a special case.
-        // TruncateInterstageVariables transform is trying to solve the HLSL compiler register
-        // mismatch issue. So it is not needed if no register is assigned to any interstage
-        // variables. As a result we only add this transform when there is at least one interstage
-        // locations being used.
+        // being used in the next stage. Still, HLSL compiler register mismatch could happen, if
+        // there's builtin inputs used in the next stage. So we still run
+        // TruncateInterstageVariables transform.
 
         // TruncateInterstageVariables itself will skip when interstage_locations matches exactly
         // with the current stage output.