diff --git a/package-lock.json b/package-lock.json
index b435177e9d..ce46cbb8b8 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,6 +1,6 @@
 {
   "name": "svelte",
-  "version": "3.0.0-alpha12",
+  "version": "3.0.0-alpha13",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
@@ -2806,20 +2806,12 @@
       "dev": true
     },
     "is-reference": {
-      "version": "1.1.0",
-      "resolved": "https://registry.npmjs.org/is-reference/-/is-reference-1.1.0.tgz",
-      "integrity": "sha512-h37O/IX4efe56o9k41II1ECMqKwtqHa7/12dLDEzJIFux2x15an4WCDb0/eKdmUgRpLJ3bR0DrzDc7vOrVgRDw==",
+      "version": "1.1.1",
+      "resolved": "https://registry.npmjs.org/is-reference/-/is-reference-1.1.1.tgz",
+      "integrity": "sha512-URlByVARcyP2E2GC7d3Ur702g3vqW391VKCHuF5Goo/M8IT97k4RU/+56OYImwDdX1J/V/VRxECE/wJqB0I2tg==",
       "dev": true,
       "requires": {
-        "@types/estree": "0.0.38"
-      },
-      "dependencies": {
-        "@types/estree": {
-          "version": "0.0.38",
-          "resolved": "https://registry.npmjs.org/@types/estree/-/estree-0.0.38.tgz",
-          "integrity": "sha512-F/v7t1LwS4vnXuPooJQGBRKRGIoxWUTmA4VHfqjOccFsNDThD5bfUNpITive6s352O7o384wcpEaDV8rHCehDA==",
-          "dev": true
-        }
+        "@types/estree": "0.0.39"
       }
     },
     "is-typedarray": {
diff --git a/package.json b/package.json
index a519b784c9..ba5512f589 100644
--- a/package.json
+++ b/package.json
@@ -63,7 +63,7 @@
     "eslint-plugin-html": "^4.0.3",
     "eslint-plugin-import": "^2.11.0",
     "estree-walker": "^0.6.0",
-    "is-reference": "^1.1.0",
+    "is-reference": "^1.1.1",
     "jsdom": "^11.8.0",
     "kleur": "^3.0.0",
     "locate-character": "^2.0.5",
diff --git a/src/compile/Component.ts b/src/compile/Component.ts
index 3118d8fa08..541814a1ff 100644
--- a/src/compile/Component.ts
+++ b/src/compile/Component.ts
@@ -539,9 +539,43 @@ export default class Component {
 		this.extract_imports_and_exports(script.content, this.imports, this.props);
 		this.hoist_instance_declarations();
 		this.extract_reactive_declarations();
+		this.extract_reactive_store_references();
 		this.javascript = this.extract_javascript(script);
 	}
 
+	extract_reactive_store_references() {
+		// TODO this pattern happens a lot... can we abstract it
+		// (or better still, do fewer AST walks)?
+		const component = this;
+		let { instance_scope: scope, instance_scope_map: map } = this;
+
+		walk(this.instance_script.content, {
+			enter(node, parent) {
+				if (map.has(node)) {
+					scope = map.get(node);
+				}
+
+				if (isReference(node, parent)) {
+					const object = getObject(node);
+					const { name } = object;
+
+					if (name[0] === '$' && !scope.has(name)) {
+						component.warn_if_undefined(object, null);
+
+						// cheeky hack
+						component.template_references.add(name);
+					}
+				}
+			},
+
+			leave(node) {
+				if (map.has(node)) {
+					scope = scope.parent;
+				}
+			}
+		});
+	}
+
 	rewrite_props() {
 		const component = this;
 		const { code, instance_scope, instance_scope_map: map, meta } = this;
@@ -735,7 +769,11 @@ export default class Component {
 						const { name } = flattenReference(node);
 						const owner = scope.findOwner(name);
 
-						if (owner === instance_scope) {
+						if (name[0] === '$' && !owner) {
+							hoistable = false;
+						}
+
+						else if (owner === instance_scope) {
 							if (name === fn_declaration.id.name) return;
 							if (hoistable_names.has(name)) return;
 							if (imported_declarations.has(name)) return;
@@ -818,13 +856,7 @@ export default class Component {
 							const object = getObject(node);
 							const { name } = object;
 
-							if (component.declarations.indexOf(name) !== -1) {
-								dependencies.add(name);
-							} else if (name[0] === '$') {
-								component.warn_if_undefined(object, null);
-
-								// cheeky hack
-								component.template_references.add(name);
+							if (name[0] === '$' || component.declarations.indexOf(name) !== -1) {
 								dependencies.add(name);
 							}
 
diff --git a/test/runtime/samples/store-auto-subscribe-in-script/_config.js b/test/runtime/samples/store-auto-subscribe-in-script/_config.js
new file mode 100644
index 0000000000..a7a8ef8d27
--- /dev/null
+++ b/test/runtime/samples/store-auto-subscribe-in-script/_config.js
@@ -0,0 +1,26 @@
+import { writable } from '../../../../store.js';
+
+const count = writable(0);
+
+export default {
+	props: {
+		count
+	},
+
+	html: `
+		<button>+1</button>
+	`,
+
+	async test({ assert, component, target, window }) {
+		assert.equal(component.get_count(), 0);
+
+		const button = target.querySelector('button');
+		const click = new window.MouseEvent('click');
+
+		await button.dispatchEvent(click);
+		assert.equal(component.get_count(), 1);
+
+		await count.set(42);
+		assert.equal(component.get_count(), 42);
+	}
+};
\ No newline at end of file
diff --git a/test/runtime/samples/store-auto-subscribe-in-script/main.html b/test/runtime/samples/store-auto-subscribe-in-script/main.html
new file mode 100644
index 0000000000..b47bddf9c1
--- /dev/null
+++ b/test/runtime/samples/store-auto-subscribe-in-script/main.html
@@ -0,0 +1,9 @@
+<script>
+	export let count;
+
+	export function get_count() {
+		return $count;
+	}
+</script>
+
+<button on:click="{() => count.update(n => n + 1)}">+1</button>
\ No newline at end of file