diff --git a/modules/@angular/compiler-cli/src/codegen.ts b/modules/@angular/compiler-cli/src/codegen.ts
index b439fed53a..8e597f1173 100644
--- a/modules/@angular/compiler-cli/src/codegen.ts
+++ b/modules/@angular/compiler-cli/src/codegen.ts
@@ -18,6 +18,7 @@ import * as ts from 'typescript';
 
 import {CompileMetadataResolver, DirectiveNormalizer, DomElementSchemaRegistry, HtmlParser, Lexer, NgModuleCompiler, Parser, StyleCompiler, TemplateParser, TypeScriptEmitter, ViewCompiler} from './compiler_private';
 import {Console} from './core_private';
+import {PathMappedReflectorHost} from './path_mapped_reflector_host';
 import {ReflectorHost, ReflectorHostContext} from './reflector_host';
 import {StaticAndDynamicReflectionCapabilities} from './static_reflection_capabilities';
 import {StaticReflector, StaticSymbol} from './static_reflector';
@@ -93,8 +94,9 @@ export class CodeGenerator {
   }
 
   codegen(): Promise<any> {
-    const filePaths =
-        this.program.getSourceFiles().map(sf => sf.fileName).filter(f => !GENERATED_FILES.test(f));
+    const filePaths = this.program.getSourceFiles()
+                          .map(sf => this.reflectorHost.getCanonicalFileName(sf.fileName))
+                          .filter(f => !GENERATED_FILES.test(f));
     const fileMetas = filePaths.map((filePath) => this.readFileMetadata(filePath));
     const ngModules = fileMetas.reduce((ngModules, fileMeta) => {
       ngModules.push(...fileMeta.ngModules);
@@ -141,7 +143,10 @@ export class CodeGenerator {
     }
 
     const urlResolver: compiler.UrlResolver = compiler.createOfflineCompileUrlResolver();
-    const reflectorHost = new ReflectorHost(program, compilerHost, options, reflectorHostContext);
+    const usePathMapping = !!options.rootDirs && options.rootDirs.length > 0;
+    const reflectorHost = usePathMapping ?
+        new PathMappedReflectorHost(program, compilerHost, options, reflectorHostContext) :
+        new ReflectorHost(program, compilerHost, options, reflectorHostContext);
     const staticReflector = new StaticReflector(reflectorHost);
     StaticAndDynamicReflectionCapabilities.install(staticReflector);
     const htmlParser =
diff --git a/modules/@angular/compiler-cli/src/path_mapped_reflector_host.ts b/modules/@angular/compiler-cli/src/path_mapped_reflector_host.ts
new file mode 100644
index 0000000000..d72eb5bf58
--- /dev/null
+++ b/modules/@angular/compiler-cli/src/path_mapped_reflector_host.ts
@@ -0,0 +1,136 @@
+/**
+ * @license
+ * Copyright Google Inc. All Rights Reserved.
+ *
+ * Use of this source code is governed by an MIT-style license that can be
+ * found in the LICENSE file at https://angular.io/license
+ */
+
+import {AngularCompilerOptions, ModuleMetadata} from '@angular/tsc-wrapped';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as ts from 'typescript';
+
+import {ReflectorHost, ReflectorHostContext} from './reflector_host';
+import {StaticSymbol} from './static_reflector';
+
+const EXT = /(\.ts|\.d\.ts|\.js|\.jsx|\.tsx)$/;
+const DTS = /\.d\.ts$/;
+
+/**
+ * This version of the reflector host expects that the program will be compiled
+ * and executed with a "path mapped" directory structure, where generated files
+ * are in a parallel tree with the sources, and imported using a `./` relative
+ * import. This requires using TS `rootDirs` option and also teaching the module
+ * loader what to do.
+ */
+export class PathMappedReflectorHost extends ReflectorHost {
+  constructor(
+      program: ts.Program, compilerHost: ts.CompilerHost, options: AngularCompilerOptions,
+      context?: ReflectorHostContext) {
+    super(program, compilerHost, options, context);
+  }
+
+  getCanonicalFileName(fileName: string): string {
+    if (!fileName) return fileName;
+    // NB: the rootDirs should have been sorted longest-first
+    for (let dir of this.options.rootDirs || []) {
+      if (fileName.indexOf(dir) === 0) {
+        fileName = fileName.substring(dir.length);
+      }
+    }
+    return fileName;
+  }
+
+  protected resolve(m: string, containingFile: string) {
+    for (const root of this.options.rootDirs || ['']) {
+      const rootedContainingFile = path.join(root, containingFile);
+      const resolved =
+          ts.resolveModuleName(m, rootedContainingFile, this.options, this.context).resolvedModule;
+      if (resolved) {
+        if (this.options.traceResolution) {
+          console.log('resolve', m, containingFile, '=>', resolved.resolvedFileName);
+        }
+        return resolved.resolvedFileName;
+      }
+    }
+  }
+
+  /**
+   * We want a moduleId that will appear in import statements in the generated code.
+   * These need to be in a form that system.js can load, so absolute file paths don't work.
+   * Relativize the paths by checking candidate prefixes of the absolute path, to see if
+   * they are resolvable by the moduleResolution strategy from the CompilerHost.
+   */
+  getImportPath(containingFile: string, importedFile: string): string {
+    importedFile = this.resolveAssetUrl(importedFile, containingFile);
+    containingFile = this.resolveAssetUrl(containingFile, '');
+
+    if (this.options.traceResolution) {
+      console.log(
+          'getImportPath from containingFile', containingFile, 'to importedFile', importedFile);
+    }
+
+    // If a file does not yet exist (because we compile it later), we still need to
+    // assume it exists so that the `resolve` method works!
+    if (!this.context.fileExists(importedFile)) {
+      this.context.assumeFileExists(importedFile);
+    }
+
+    const resolvable = (candidate: string) => {
+      const resolved = this.getCanonicalFileName(this.resolve(candidate, importedFile));
+      return resolved && resolved.replace(EXT, '') === importedFile.replace(EXT, '');
+    };
+
+    let importModuleName = importedFile.replace(EXT, '');
+    const parts = importModuleName.split(path.sep).filter(p => !!p);
+    let foundRelativeImport: string;
+    for (let index = parts.length - 1; index >= 0; index--) {
+      let candidate = parts.slice(index, parts.length).join(path.sep);
+      if (resolvable(candidate)) {
+        return candidate;
+      }
+      candidate = '.' + path.sep + candidate;
+      if (resolvable(candidate)) {
+        foundRelativeImport = candidate;
+      }
+    }
+
+    if (foundRelativeImport) return foundRelativeImport;
+
+    // Try a relative import
+    const candidate = path.relative(path.dirname(containingFile), importModuleName);
+    if (resolvable(candidate)) {
+      return candidate;
+    }
+
+    throw new Error(
+        `Unable to find any resolvable import for ${importedFile} relative to ${containingFile}`);
+  }
+
+  getMetadataFor(filePath: string): ModuleMetadata {
+    for (const root of this.options.rootDirs || []) {
+      const rootedPath = path.join(root, filePath);
+      if (!this.compilerHost.fileExists(rootedPath)) {
+        // If the file doesn't exists then we cannot return metadata for the file.
+        // This will occur if the user refernced a declared module for which no file
+        // exists for the module (i.e. jQuery or angularjs).
+        continue;
+      }
+      if (DTS.test(rootedPath)) {
+        const metadataPath = rootedPath.replace(DTS, '.metadata.json');
+        if (this.context.fileExists(metadataPath)) {
+          const metadata = this.readMetadata(metadataPath);
+          return (Array.isArray(metadata) && metadata.length == 0) ? undefined : metadata;
+        }
+      } else {
+        const sf = this.program.getSourceFile(rootedPath);
+        if (!sf) {
+          throw new Error(`Source file ${rootedPath} not present in program.`);
+        }
+        sf.fileName = this.getCanonicalFileName(sf.fileName);
+        return this.metadataCollector.getMetadata(sf);
+      }
+    }
+  }
+}
diff --git a/modules/@angular/compiler-cli/src/reflector_host.ts b/modules/@angular/compiler-cli/src/reflector_host.ts
index ce56d96473..2011c2c80a 100644
--- a/modules/@angular/compiler-cli/src/reflector_host.ts
+++ b/modules/@angular/compiler-cli/src/reflector_host.ts
@@ -27,14 +27,14 @@ export interface ReflectorHostContext {
 }
 
 export class ReflectorHost implements StaticReflectorHost, ImportGenerator {
-  private metadataCollector = new MetadataCollector();
-  private context: ReflectorHostContext;
+  protected metadataCollector = new MetadataCollector();
+  protected context: ReflectorHostContext;
   private isGenDirChildOfRootDir: boolean;
-  private basePath: string;
+  protected basePath: string;
   private genDir: string;
   constructor(
-      private program: ts.Program, private compilerHost: ts.CompilerHost,
-      private options: AngularCompilerOptions, context?: ReflectorHostContext) {
+      protected program: ts.Program, protected compilerHost: ts.CompilerHost,
+      protected options: AngularCompilerOptions, context?: ReflectorHostContext) {
     // normalize the path so that it never ends with '/'.
     this.basePath = path.normalize(path.join(this.options.basePath, '.'));
     this.genDir = path.normalize(path.join(this.options.genDir, '.'));
@@ -55,21 +55,25 @@ export class ReflectorHost implements StaticReflectorHost, ImportGenerator {
     };
   }
 
-  private resolve(m: string, containingFile: string) {
+  // We use absolute paths on disk as canonical.
+  getCanonicalFileName(fileName: string): string { return fileName; }
+
+  protected resolve(m: string, containingFile: string) {
     const resolved =
         ts.resolveModuleName(m, containingFile, this.options, this.context).resolvedModule;
     return resolved ? resolved.resolvedFileName : null;
   };
 
-  private normalizeAssetUrl(url: string): string {
+  protected normalizeAssetUrl(url: string): string {
     let assetUrl = AssetUrl.parse(url);
-    return assetUrl ? `${assetUrl.packageName}/${assetUrl.modulePath}` : null;
+    const path = assetUrl ? `${assetUrl.packageName}/${assetUrl.modulePath}` : null;
+    return this.getCanonicalFileName(path);
   }
 
-  private resolveAssetUrl(url: string, containingFile: string): string {
+  protected resolveAssetUrl(url: string, containingFile: string): string {
     let assetUrl = this.normalizeAssetUrl(url);
     if (assetUrl) {
-      return this.resolve(assetUrl, containingFile);
+      return this.getCanonicalFileName(this.resolve(assetUrl, containingFile));
     }
     return url;
   }
@@ -198,7 +202,7 @@ export class ReflectorHost implements StaticReflectorHost, ImportGenerator {
         symbol = tc.getAliasedSymbol(symbol);
       }
       const declaration = symbol.getDeclarations()[0];
-      const declarationFile = declaration.getSourceFile().fileName;
+      const declarationFile = this.getCanonicalFileName(declaration.getSourceFile().fileName);
 
       return this.getStaticSymbol(declarationFile, symbol.getName());
     } catch (e) {
@@ -267,9 +271,9 @@ export class ReflectorHost implements StaticReflectorHost, ImportGenerator {
     return metadata;
   }
 
-  private resolveExportedSymbol(filePath: string, symbolName: string): StaticSymbol {
+  protected resolveExportedSymbol(filePath: string, symbolName: string): StaticSymbol {
     const resolveModule = (moduleName: string): string => {
-      const resolvedModulePath = this.resolve(moduleName, filePath);
+      const resolvedModulePath = this.getCanonicalFileName(this.resolve(moduleName, filePath));
       if (!resolvedModulePath) {
         throw new Error(`Could not resolve module '${moduleName}' relative to file ${filePath}`);
       }