diff --git a/src/Bundle.js b/src/Bundle.js
index 1c28ce3..07a788c 100644
--- a/src/Bundle.js
+++ b/src/Bundle.js
@@ -15,7 +15,7 @@ import transformBundle from './utils/transformBundle.js';
 import collapseSourcemaps from './utils/collapseSourcemaps.js';
 import SOURCEMAPPING_URL from './utils/sourceMappingURL.js';
 import callIfFunction from './utils/callIfFunction.js';
-import { isRelative, resolve } from './utils/path.js';
+import { dirname, isRelative, relative, resolve } from './utils/path.js';
 
 export default class Bundle {
 	constructor ( options ) {
@@ -28,6 +28,7 @@ export default class Bundle {
 		});
 
 		this.entry = unixizePath( options.entry );
+		this.entryId = null;
 		this.entryModule = null;
 
 		this.resolveId = first(
@@ -71,7 +72,10 @@ export default class Bundle {
 		// modules it imports, and import those, until we have all
 		// of the entry module's dependencies
 		return this.resolveId( this.entry, undefined )
-			.then( id => this.fetchModule( id, undefined ) )
+			.then( id => {
+				this.entryId = id;
+				return this.fetchModule( id, undefined );
+			})
 			.then( entryModule => {
 				this.entryModule = entryModule;
 
@@ -189,16 +193,20 @@ export default class Bundle {
 					const forcedExternal = externalName && ~this.external.indexOf( externalName );
 
 					if ( !resolvedId || forcedExternal ) {
+						let normalizedExternal = source;
+
 						if ( !forcedExternal ) {
 							if ( isRelative( source ) ) throw new Error( `Could not resolve ${source} from ${module.id}` );
 							if ( !~this.external.indexOf( source ) ) this.onwarn( `Treating '${source}' as external dependency` );
+						} else if ( resolvedId ) {
+							normalizedExternal = this.getPathRelativeToEntryDirname( resolvedId );
 						}
-						module.resolvedIds[ source ] = source;
+						module.resolvedIds[ source ] = normalizedExternal;
 
-						if ( !this.moduleById[ source ] ) {
-							const module = new ExternalModule( source );
+						if ( !this.moduleById[ normalizedExternal ] ) {
+							const module = new ExternalModule( normalizedExternal );
 							this.externalModules.push( module );
-							this.moduleById[ source ] = module;
+							this.moduleById[ normalizedExternal ] = module;
 						}
 					}
 
@@ -214,6 +222,19 @@ export default class Bundle {
 		});
 	}
 
+	getPathRelativeToEntryDirname ( resolvedId ) {
+		// Get a path relative to the resolved entry directory
+		const entryDirname = dirname( this.entryId );
+		const relativeToEntry = relative( entryDirname, resolvedId );
+
+		if ( isRelative( relativeToEntry )) {
+			return relativeToEntry;
+		}
+
+		// The path is missing the `./` prefix
+		return `./${relativeToEntry}`;
+	}
+
 	render ( options = {} ) {
 		const format = options.format || 'es6';
 
diff --git a/test/function/relative-external-include-once-nested/_config.js b/test/function/relative-external-include-once-nested/_config.js
new file mode 100644
index 0000000..07aa08e
--- /dev/null
+++ b/test/function/relative-external-include-once-nested/_config.js
@@ -0,0 +1,18 @@
+var assert = require( 'assert' );
+var path = require( 'path' );
+
+module.exports = {
+	description: 'includes a relative external module only once (nested version)',
+	options: {
+		external: path.join( __dirname, './first/foo.js' )
+	},
+	context: {
+		require: function ( required ) {
+			assert.equal( required, './first/foo.js' );
+			return 1;
+		}
+	},
+	exports: function ( exports ) {
+		assert.equal( exports, 3 );
+	}
+};
diff --git a/test/function/relative-external-include-once-nested/first/foo.js b/test/function/relative-external-include-once-nested/first/foo.js
new file mode 100644
index 0000000..e69de29
diff --git a/test/function/relative-external-include-once-nested/first/module.js b/test/function/relative-external-include-once-nested/first/module.js
new file mode 100644
index 0000000..a0aecca
--- /dev/null
+++ b/test/function/relative-external-include-once-nested/first/module.js
@@ -0,0 +1,4 @@
+import foo from './foo';
+import second from './second/module';
+
+export default foo + second;
diff --git a/test/function/relative-external-include-once-nested/first/second/module.js b/test/function/relative-external-include-once-nested/first/second/module.js
new file mode 100644
index 0000000..4fa8fdc
--- /dev/null
+++ b/test/function/relative-external-include-once-nested/first/second/module.js
@@ -0,0 +1,3 @@
+import foo from '../foo';
+
+export default foo;
diff --git a/test/function/relative-external-include-once-nested/main.js b/test/function/relative-external-include-once-nested/main.js
new file mode 100644
index 0000000..545e333
--- /dev/null
+++ b/test/function/relative-external-include-once-nested/main.js
@@ -0,0 +1,4 @@
+import foo from './first/foo';
+import first from './first/module';
+
+export default foo + first;
diff --git a/test/function/relative-external-include-once-two-external/_config.js b/test/function/relative-external-include-once-two-external/_config.js
new file mode 100644
index 0000000..d83e72f
--- /dev/null
+++ b/test/function/relative-external-include-once-two-external/_config.js
@@ -0,0 +1,22 @@
+var assert = require( 'assert' );
+var path = require( 'path' );
+
+
+module.exports = {
+	description: 'includes a relative external module only once (two external deps)',
+	options: {
+		external: [
+			path.join( __dirname, './foo.js' ),
+			path.join( __dirname, './first/foo.js' )
+		]
+	},
+	context: {
+		require: function ( required ) {
+			assert( [ './foo.js', './first/foo.js' ].indexOf(required) !== -1, 'required wrong module' );
+			return required === './foo.js' ? 'a' : 'b';
+		}
+	},
+	exports: function ( exports ) {
+		assert( exports === 'ab' || exports === 'ba', 'two different modules should be required' );
+	}
+};
diff --git a/test/function/relative-external-include-once-two-external/first/foo.js b/test/function/relative-external-include-once-two-external/first/foo.js
new file mode 100644
index 0000000..e69de29
diff --git a/test/function/relative-external-include-once-two-external/first/module.js b/test/function/relative-external-include-once-two-external/first/module.js
new file mode 100644
index 0000000..4ad6554
--- /dev/null
+++ b/test/function/relative-external-include-once-two-external/first/module.js
@@ -0,0 +1,3 @@
+import foo from './foo';
+
+export default foo;
diff --git a/test/function/relative-external-include-once-two-external/foo.js b/test/function/relative-external-include-once-two-external/foo.js
new file mode 100644
index 0000000..e69de29
diff --git a/test/function/relative-external-include-once-two-external/main.js b/test/function/relative-external-include-once-two-external/main.js
new file mode 100644
index 0000000..dff375c
--- /dev/null
+++ b/test/function/relative-external-include-once-two-external/main.js
@@ -0,0 +1,4 @@
+import foo from './foo';
+import first from './first/module';
+
+export default foo + first;
diff --git a/test/function/relative-external-include-once-up/_config.js b/test/function/relative-external-include-once-up/_config.js
new file mode 100644
index 0000000..15821ba
--- /dev/null
+++ b/test/function/relative-external-include-once-up/_config.js
@@ -0,0 +1,19 @@
+var assert = require( 'assert' );
+var path = require( 'path' );
+
+module.exports = {
+	description: 'includes a relative external module only once (from upper directory too)',
+	options: {
+		entry: path.join( __dirname, 'first', 'main.js' ),
+		external: path.join( __dirname, './foo.js' )
+	},
+	context: {
+		require: function ( required ) {
+			assert.equal( required, '../foo.js' );
+			return 1;
+		}
+	},
+	exports: function ( exports ) {
+		assert.equal( exports, 3 );
+	}
+};
diff --git a/test/function/relative-external-include-once-up/first/main.js b/test/function/relative-external-include-once-up/first/main.js
new file mode 100644
index 0000000..a07e358
--- /dev/null
+++ b/test/function/relative-external-include-once-up/first/main.js
@@ -0,0 +1,4 @@
+import foo from '../foo';
+import first from './module';
+
+export default foo + first;
diff --git a/test/function/relative-external-include-once-up/first/module.js b/test/function/relative-external-include-once-up/first/module.js
new file mode 100644
index 0000000..0798b47
--- /dev/null
+++ b/test/function/relative-external-include-once-up/first/module.js
@@ -0,0 +1,4 @@
+import foo from '../foo';
+import second from './second/module';
+
+export default foo + second;
diff --git a/test/function/relative-external-include-once-up/first/second/module.js b/test/function/relative-external-include-once-up/first/second/module.js
new file mode 100644
index 0000000..b643f0c
--- /dev/null
+++ b/test/function/relative-external-include-once-up/first/second/module.js
@@ -0,0 +1,3 @@
+import foo from '../../foo';
+
+export default foo;
diff --git a/test/function/relative-external-include-once-up/foo.js b/test/function/relative-external-include-once-up/foo.js
new file mode 100644
index 0000000..e69de29
diff --git a/test/function/relative-external-include-once/_config.js b/test/function/relative-external-include-once/_config.js
new file mode 100644
index 0000000..4349dc1
--- /dev/null
+++ b/test/function/relative-external-include-once/_config.js
@@ -0,0 +1,18 @@
+var assert = require( 'assert' );
+var path = require( 'path' );
+
+module.exports = {
+	description: 'includes a relative external module only once',
+	options: {
+		external: path.join( __dirname, './foo.js' )
+	},
+	context: {
+		require: function ( required ) {
+			assert.equal( required, './foo.js' );
+			return 1;
+		}
+	},
+	exports: function ( exports ) {
+		assert.equal( exports, 3 );
+	}
+};
diff --git a/test/function/relative-external-include-once/first/module.js b/test/function/relative-external-include-once/first/module.js
new file mode 100644
index 0000000..0798b47
--- /dev/null
+++ b/test/function/relative-external-include-once/first/module.js
@@ -0,0 +1,4 @@
+import foo from '../foo';
+import second from './second/module';
+
+export default foo + second;
diff --git a/test/function/relative-external-include-once/first/second/module.js b/test/function/relative-external-include-once/first/second/module.js
new file mode 100644
index 0000000..b643f0c
--- /dev/null
+++ b/test/function/relative-external-include-once/first/second/module.js
@@ -0,0 +1,3 @@
+import foo from '../../foo';
+
+export default foo;
diff --git a/test/function/relative-external-include-once/foo.js b/test/function/relative-external-include-once/foo.js
new file mode 100644
index 0000000..e69de29
diff --git a/test/function/relative-external-include-once/main.js b/test/function/relative-external-include-once/main.js
new file mode 100644
index 0000000..dff375c
--- /dev/null
+++ b/test/function/relative-external-include-once/main.js
@@ -0,0 +1,4 @@
+import foo from './foo';
+import first from './first/module';
+
+export default foo + first;
diff --git a/test/test.js b/test/test.js
index 39a81fc..358e390 100644
--- a/test/test.js
+++ b/test/test.js
@@ -133,9 +133,9 @@ describe( 'rollup', function () {
 
 			var config = loadConfig( FUNCTION + '/' + dir + '/_config.js' );
 			( config.skip ? it.skip : config.solo ? it.only : it )( dir, function () {
-				var options = extend( {}, config.options, {
+				var options = extend( {
 					entry: FUNCTION + '/' + dir + '/main.js'
-				});
+				}, config.options );
 
 				if ( config.solo ) console.group( dir );