diff --git a/docs/hooks.md b/docs/hooks.md
index 6ca7a6d1..19411c7c 100644
--- a/docs/hooks.md
+++ b/docs/hooks.md
@@ -57,7 +57,7 @@ This function downloads and executes the code for a module. The promise must res
 
 The default system.js implementation is to append a script tag that downloads and executes the module's code, subsequently resolving the promise with the most recent register: `resolve(System.getRegister())`. [Example](https://github.com/systemjs/systemjs/blob/master/src/features/script-load.js).
 
-#### getRegister() -> [deps: String[], declare: Function]
+#### getRegister(url) -> [deps: String[], declare: Function]
 
 > This hook is intended for custom module format integrations only.
 
diff --git a/src/extras/named-register.js b/src/extras/named-register.js
index 9706a1d1..1d3e4631 100644
--- a/src/extras/named-register.js
+++ b/src/extras/named-register.js
@@ -17,10 +17,11 @@
   SystemJS.prototype = systemJSPrototype;
   System.constructor = SystemJS;
 
-  var firstNamedDefine;
+  var firstNamedDefine, firstName;
 
   function setRegisterRegistry(systemInstance) {
     systemInstance.registerRegistry = Object.create(null);
+    systemInstance.namedRegisterAliases = Object.create(null);
   }
 
   var register = systemJSPrototype.register;
@@ -31,10 +32,12 @@
     this.registerRegistry[name] = define;
     if (!firstNamedDefine) {
       firstNamedDefine = define;
-      Promise.resolve().then(function () {
-        firstNamedDefine = null;
-      });
+      firstName = name;
     }
+    setTimeout(function () {
+      firstNamedDefine = null;
+      firstName = null;
+    });
     return register.apply(this, [deps, declare]);
   };
 
@@ -45,7 +48,7 @@
       return resolve.call(this, id, parentURL);
     } catch (err) {
       if (id in this.registerRegistry) {
-        return id;
+        return this.namedRegisterAliases[id] || id;
       }
       throw err;
     }
@@ -63,12 +66,16 @@
   };
 
   var getRegister = systemJSPrototype.getRegister;
-  systemJSPrototype.getRegister = function () {
+  systemJSPrototype.getRegister = function (url) {
     // Calling getRegister() because other extras need to know it was called so they can perform side effects
-    var register = getRegister.call(this);
+    var register = getRegister.call(this, url);
 
+    if (firstName && url) {
+      this.namedRegisterAliases[firstName] = url;
+    }
     var result = firstNamedDefine || register;
     firstNamedDefine = null;
+    firstName = null;
     return result;
   }
 })(typeof self !== 'undefined' ? self : global);
diff --git a/src/extras/transform.js b/src/extras/transform.js
index 9caf6d51..da34fb5f 100644
--- a/src/extras/transform.js
+++ b/src/extras/transform.js
@@ -25,7 +25,7 @@ import { errMsg } from '../err-msg.js';
     })
     .then(function (source) {
       (0, eval)(source + '\n//# sourceURL=' + url);
-      return loader.getRegister();
+      return loader.getRegister(url);
     });
   };
 
diff --git a/src/features/fetch-load.js b/src/features/fetch-load.js
index 5dce9d38..d00c5c6e 100644
--- a/src/features/fetch-load.js
+++ b/src/features/fetch-load.js
@@ -31,7 +31,7 @@ systemJSPrototype.instantiate = function (url, parent) {
       if (source.indexOf('//# sourceURL=') < 0)
         source += '\n//# sourceURL=' + url;
       (0, eval)(source);
-      return loader.getRegister();
+      return loader.getRegister(url);
     });
   });
 };
diff --git a/src/features/script-load.js b/src/features/script-load.js
index ee7db6be..bace6f8b 100644
--- a/src/features/script-load.js
+++ b/src/features/script-load.js
@@ -76,7 +76,7 @@ systemJSPrototype.instantiate = function (url, firstParentUrl) {
         reject(lastWindowError);
       }
       else {
-        var register = loader.getRegister();
+        var register = loader.getRegister(url);
         // Clear any auto import registration for dynamic import scripts during load
         if (register && register[0] === lastAutoImportDeps)
           clearTimeout(lastAutoImportTimeout);
diff --git a/src/features/worker-load.js b/src/features/worker-load.js
index 9e8d7403..c0171b33 100644
--- a/src/features/worker-load.js
+++ b/src/features/worker-load.js
@@ -9,6 +9,6 @@ if (hasSelf && typeof importScripts === 'function')
     var loader = this;
     return Promise.resolve().then(function () {
       importScripts(url);
-      return loader.getRegister();
+      return loader.getRegister(url);
     });
   };
diff --git a/test/browser/named-register.js b/test/browser/named-register.js
index a508c95b..490f5b90 100644
--- a/test/browser/named-register.js
+++ b/test/browser/named-register.js
@@ -171,4 +171,30 @@ suite('Named System.register', function() {
       assert.equal(m.b, 'b');
     });
   });
+
+  // https://github.com/systemjs/systemjs/issues/2349
+  test('Bundles with named register do not instantiate last module more than once', function () {
+    // First import the module via URL
+    return System.import('./fixtures/browser/named-instantiate-count.js').then(function (urlModule) {
+      // Then import the same module via named register name
+      return System.import('named-instantiate-count').then(function (namedModule) {
+        assert.equal(urlModule.getInstantiateCount(), 1);
+        assert.equal(namedModule.getInstantiateCount(), 1);
+        assert.equal(urlModule, namedModule);
+      });
+    });
+  });
+
+  // https://github.com/systemjs/systemjs/issues/2349
+  test('Named bundles that self import', function () {
+    // First import the module via URL
+    return System.import('./fixtures/browser/named-self-import.js').then(function (urlModule) {
+      // Then import the same module via named register name
+      return System.import('named-self-import').then(function (namedModule) {
+        assert.equal(urlModule.getInstantiateCount(), 1);
+        assert.equal(namedModule.getInstantiateCount(), 1);
+        assert.equal(urlModule, namedModule);
+      });
+    });
+  });
 });
\ No newline at end of file
diff --git a/test/fixtures/browser/named-instantiate-count.js b/test/fixtures/browser/named-instantiate-count.js
new file mode 100644
index 00000000..e0839e2a
--- /dev/null
+++ b/test/fixtures/browser/named-instantiate-count.js
@@ -0,0 +1,12 @@
+let instantiateCount = 0;
+
+System.register("named-instantiate-count", [], function (_export) {
+  instantiateCount++;
+  return {
+    execute: function () {
+      _export('getInstantiateCount', function () {
+        return instantiateCount;
+      });
+    }
+  };
+});
\ No newline at end of file
diff --git a/test/fixtures/browser/named-self-import.js b/test/fixtures/browser/named-self-import.js
new file mode 100644
index 00000000..468335d7
--- /dev/null
+++ b/test/fixtures/browser/named-self-import.js
@@ -0,0 +1,31 @@
+let instantiateCount = 0;
+
+System.register("named-self-import", ["named-self-import/dep"], function (_export) {
+  instantiateCount++;
+  var dep;
+
+  return {
+    setters: [
+      function (d) {
+        dep = d;
+      }
+    ],
+    execute: function () {
+      dep.method();
+
+      _export('getInstantiateCount', function () {
+        return instantiateCount;
+      });
+    }
+  };
+});
+
+System.register("named-self-import/dep", [], function (_export) {
+  return {
+    execute: function () {
+      _export("method", function () {
+        return 1;
+      });
+    }
+  };
+});