diff --git a/src/lib/settings.html b/src/lib/settings.html
index 77eccef239..7e4c4288f7 100644
--- a/src/lib/settings.html
+++ b/src/lib/settings.html
@@ -38,6 +38,8 @@
       var useNativeCustomElements = (!window.CustomElements ||
         window.CustomElements.useNative);
 
+      var usePolyfillProto = !useNativeCustomElements && !Object.__proto__;
+
       return {
         wantShadow: wantShadow,
         hasShadow: hasShadow,
@@ -45,7 +47,8 @@
         useShadow: useShadow,
         useNativeShadow: useShadow && nativeShadow,
         useNativeImports: useNativeImports,
-        useNativeCustomElements: useNativeCustomElements
+        useNativeCustomElements: useNativeCustomElements,
+        usePolyfillProto: usePolyfillProto
       };
     })()
   };
diff --git a/src/standard/configure.html b/src/standard/configure.html
index 0619bad2d0..b994b00367 100644
--- a/src/standard/configure.html
+++ b/src/standard/configure.html
@@ -9,7 +9,7 @@
 -->
 
 <script>
-
+(function() {
   /*
     Process inputs efficiently via a configure lifecycle callback.
     Configure is called top-down, host before local dom. Users should
@@ -41,6 +41,8 @@
   directly (on-foo-changed).
   */
 
+  var usePolyfillProto = Polymer.Settings.usePolyfillProto;
+
   Polymer.Base._addFeature({
 
     // storage for configuration
@@ -118,7 +120,7 @@
         // to override default values. This allows late upgrade + an early set
         // to not b0rk accessors on the prototype.
         // Perf testing has shown `hasOwnProperty` to be ok here.
-        if (this.hasOwnProperty(i)) {
+        if (!usePolyfillProto && this.hasOwnProperty(i)) {
           config[i] = this[i];
           delete this[i];
         } else if (c.value !== undefined) {
@@ -223,4 +225,5 @@
 
   });
 
+})();
 </script>
diff --git a/test/unit/configure.html b/test/unit/configure.html
index a51a1d7597..dc125a89a0 100644
--- a/test/unit/configure.html
+++ b/test/unit/configure.html
@@ -104,6 +104,10 @@
     });
 
     test('pre-register property assignment does not break getters and setters', function() {
+      // don't test if __proto__ is polyfilled (IE10); cannot be fixed in this case.
+      if (Polymer.Settings.usePolyfillProto) {
+        return;
+      }
       var x = document.createElement('x-late-register');
       document.body.appendChild(x);
       // set property