diff --git a/lib/coffee-script/coffee-script.js b/lib/coffee-script/coffee-script.js
index 03c5e738..e0129604 100644
--- a/lib/coffee-script/coffee-script.js
+++ b/lib/coffee-script/coffee-script.js
@@ -1,6 +1,6 @@
 // Generated by CoffeeScript 1.6.1
 (function() {
-  var Lexer, compile, ext, fs, helpers, lexer, loadFile, parser, path, sourcemap, vm, _i, _len, _ref,
+  var Lexer, compile, ext, fs, generateV3SourceMapOptions, helpers, lexer, loadFile, parser, path, sourcemap, vm, _i, _len, _ref,
     __hasProp = {}.hasOwnProperty;
 
   fs = require('fs');
@@ -39,16 +39,39 @@
 
   exports.helpers = helpers;
 
+  generateV3SourceMapOptions = function(options) {
+    var cwd, sourceRoot;
+    if (options == null) {
+      options = {};
+    }
+    console.log("Generating v3 source map");
+    cwd = options.workingDirectory;
+    if (!options.filename) {
+      return {};
+    }
+    if (options.jsPath) {
+      sourceRoot = helpers.relativePath(options.jsPath, ".", cwd);
+      return {
+        sourceRoot: sourceRoot,
+        sourceFile: helpers.relativePath(".", options.filename, cwd),
+        generatedFile: helpers.baseFileName(options.jsPath)
+      };
+    }
+    return {
+      sourceRoot: "",
+      sourceFile: helpers.baseFileName(options.filename),
+      generatedFile: helpers.baseFileName(options.filename, true) + ".js"
+    };
+  };
+
   exports.compile = compile = function(code, options) {
-    var answer, coffeeFile, currentColumn, currentLine, err, fragment, fragments, header, js, jsFile, merge, newLines, sourceMap, _j, _len1;
+    var answer, currentColumn, currentLine, err, fragment, fragments, header, js, merge, newLines, sourceMap, v3Options, _j, _len1;
     if (options == null) {
       options = {};
     }
     merge = exports.helpers.merge;
     try {
       if (options.sourceMap) {
-        coffeeFile = helpers.baseFileName(options.filename);
-        jsFile = helpers.baseFileName(options.filename, true) + ".js";
         sourceMap = new sourcemap.SourceMap();
       }
       fragments = (parser.parse(lexer.tokenize(code, options))).compileToFragments(options);
@@ -89,7 +112,8 @@
       };
       if (sourceMap) {
         answer.sourceMap = sourceMap;
-        answer.v3SourceMap = sourcemap.generateV3SourceMap(sourceMap, coffeeFile, jsFile);
+        v3Options = generateV3SourceMapOptions(options);
+        answer.v3SourceMap = sourcemap.generateV3SourceMap(sourceMap, v3Options);
       }
       return answer;
     } else {
diff --git a/lib/coffee-script/command.js b/lib/coffee-script/command.js
index 809dffba..bffb1e18 100644
--- a/lib/coffee-script/command.js
+++ b/lib/coffee-script/command.js
@@ -149,8 +149,11 @@
 
   compileScript = function(file, input, base) {
     var compiled, err, o, options, t, task;
+    if (base == null) {
+      base = null;
+    }
     o = opts;
-    options = compileOptions(file);
+    options = compileOptions(file, base);
     try {
       t = task = {
         file: file,
@@ -181,7 +184,7 @@
         if (o.print) {
           return printLine(t.output.trim());
         } else if (o.compile || o.map) {
-          return writeJs(base, t.file, t.output, t.sourceMap);
+          return writeJs(base, t.file, t.output, options.jsPath, t.sourceMap);
         } else if (o.lint) {
           return lint(t.file, t.output);
         }
@@ -388,12 +391,11 @@
     return path.join(dir, basename + extension);
   };
 
-  writeJs = function(base, sourcePath, js, generatedSourceMap) {
-    var compile, jsDir, jsPath, sourceMapPath;
+  writeJs = function(base, sourcePath, js, jsPath, generatedSourceMap) {
+    var compile, jsDir, sourceMapPath;
     if (generatedSourceMap == null) {
       generatedSourceMap = null;
     }
-    jsPath = outputPath(sourcePath, base);
     sourceMapPath = outputPath(sourcePath, base, ".map");
     jsDir = path.dirname(jsPath);
     compile = function() {
@@ -480,13 +482,15 @@
     }
   };
 
-  compileOptions = function(filename) {
+  compileOptions = function(filename, base) {
     return {
       filename: filename,
       literate: helpers.isLiterate(filename),
       bare: opts.bare,
       header: opts.compile,
-      sourceMap: opts.map
+      sourceMap: opts.map,
+      jsPath: filename !== null && base !== null ? outputPath(filename, base) : null,
+      workingDirectory: process.cwd()
     };
   };
 
diff --git a/lib/coffee-script/helpers.js b/lib/coffee-script/helpers.js
index 601aa7fc..bfa7e277 100644
--- a/lib/coffee-script/helpers.js
+++ b/lib/coffee-script/helpers.js
@@ -1,6 +1,6 @@
 // Generated by CoffeeScript 1.6.1
 (function() {
-  var buildLocationData, extend, flatten, _ref;
+  var buildLocationData, extend, flatten, last, normalizePath, repeat, _ref;
 
   exports.starts = function(string, literal, start) {
     return literal === string.substr(start, literal.length);
@@ -12,6 +12,19 @@
     return literal === string.substr(string.length - len - (back || 0), len);
   };
 
+  exports.repeat = repeat = function(str, n) {
+    var res;
+    res = '';
+    while (n > 0) {
+      if (n & 1) {
+        res += str;
+      }
+      n >>>= 1;
+      str += str;
+    }
+    return res;
+  };
+
   exports.compact = function(array) {
     var item, _i, _len, _results;
     _results = [];
@@ -70,7 +83,7 @@
     return val;
   };
 
-  exports.last = function(array, back) {
+  exports.last = last = function(array, back) {
     return array[array.length - (back || 0) - 1];
   };
 
@@ -166,4 +179,67 @@
     return /\.(litcoffee|coffee\.md)$/.test(file);
   };
 
+  exports.normalizePath = normalizePath = function(path, removeTrailingSlash) {
+    var i, newParts, part, parts, root, _i, _len;
+    if (removeTrailingSlash == null) {
+      removeTrailingSlash = false;
+    }
+    root = false;
+    parts = path.split('/');
+    newParts = [];
+    i = 0;
+    if (parts.length > 1 && parts[0] === '') {
+      parts.shift();
+      root = true;
+    }
+    for (i = _i = 0, _len = parts.length; _i < _len; i = ++_i) {
+      part = parts[i];
+      if (part === '.' || part === '') {
+        if ((i === parts.length - 1) && !removeTrailingSlash) {
+          newParts.push('');
+        }
+      } else if (part === '..') {
+        if (newParts.length === 0 || (newParts.length && last(newParts === '..'))) {
+          newParts.push('..');
+        } else {
+          newParts.pop();
+        }
+      } else {
+        newParts.push(part);
+      }
+    }
+    if (root) {
+      if (newParts.length === 0) {
+        return '/';
+      }
+      if (newParts.length[0] === '..') {
+        throw new Error("Invalid path: " + path);
+      }
+      newParts.unshift('');
+    }
+    return newParts.join('/');
+  };
+
+  exports.relativePath = function(from, to, cwd) {
+    var answer;
+    if (cwd == null) {
+      cwd = null;
+    }
+    if (cwd) {
+      from = cwd + "/" + from;
+      to = cwd + "/" + to;
+    }
+    from = normalizePath(from).split('/');
+    to = normalizePath(to).split('/');
+    while (from.length > 0 && to.length > 0 && from[0] === to[0]) {
+      from.shift();
+      to.shift();
+    }
+    if (from.length && from[0] === "..") {
+      throw new Error("'cwd' must be specified if 'from' references parent directory: " + (from.join('/')) + " -> " + (to.join('/')));
+    }
+    answer = repeat("../", from.length - 1);
+    return answer + ("" + (to.join('/')));
+  };
+
 }).call(this);
diff --git a/lib/coffee-script/sourcemap.js b/lib/coffee-script/sourcemap.js
index 245da945..34b18d15 100644
--- a/lib/coffee-script/sourcemap.js
+++ b/lib/coffee-script/sourcemap.js
@@ -113,14 +113,14 @@
 
   })();
 
-  exports.generateV3SourceMap = function(sourceMap, sourceFile, generatedFile) {
-    var answer, lastGeneratedColumnWritten, lastSourceColumnWritten, lastSourceLineWritten, mappings, needComma, writingGeneratedLine;
-    if (sourceFile == null) {
-      sourceFile = null;
-    }
-    if (generatedFile == null) {
-      generatedFile = null;
+  exports.generateV3SourceMap = function(sourceMap, options) {
+    var answer, generatedFile, lastGeneratedColumnWritten, lastSourceColumnWritten, lastSourceLineWritten, mappings, needComma, sourceFile, sourceRoot, writingGeneratedLine;
+    if (options == null) {
+      options = {};
     }
+    sourceRoot = options.sourceRoot || "";
+    sourceFile = options.sourceFile || null;
+    generatedFile = options.generatedFile || null;
     writingGeneratedLine = 0;
     lastGeneratedColumnWritten = 0;
     lastSourceLineWritten = 0;
@@ -150,7 +150,7 @@
     answer = {
       version: 3,
       file: generatedFile,
-      sourceRoot: "",
+      sourceRoot: sourceRoot,
       sources: sourceFile ? [sourceFile] : [],
       names: [],
       mappings: mappings
diff --git a/src/coffee-script.coffee b/src/coffee-script.coffee
index bf9a5edd..57f69e00 100644
--- a/src/coffee-script.coffee
+++ b/src/coffee-script.coffee
@@ -30,9 +30,41 @@ exports.VERSION = '1.6.1'
 # Expose helpers for testing.
 exports.helpers = helpers
 
+# Generate v3 Source Map options from compile options.
+#
+# options.filename is required, and is the path and filename of the file being compiled,
+# relative to the current working directory.
+#
+# `options.jsPath` and `options.workingDirectory` may also be specified to customize the output
+# in the resulting v3 source map, where `options.jsPath` is the path where the .js file will be
+# written relative to the current working directory, and `options.workingDirectory` is the absolute
+# path of the current working directory (required if jsPath references a parent directory.)  If
+# these options are provided, then "sourceRoot" in the output will be a relative path to the
+# current working directory, and source files will be given relative to the "sourceRoot".
+#
+generateV3SourceMapOptions = (options = {}) ->
+  console.log "Generating v3 source map"
+  cwd = options.workingDirectory
+  return {} unless options.filename
+  if options.jsPath
+    sourceRoot = helpers.relativePath options.jsPath, ".", cwd
+    return {
+      sourceRoot
+      sourceFile: helpers.relativePath ".", options.filename, cwd
+      generatedFile: helpers.baseFileName(options.jsPath)
+    }
+  {
+    sourceRoot: ""
+    sourceFile: helpers.baseFileName options.filename
+    generatedFile: helpers.baseFileName(options.filename, yes) + ".js"
+  }
+
+
 # Compile CoffeeScript code to JavaScript, using the Coffee/Jison compiler.
 #
-# If `options.sourceMap` is specified, then `options.filename` must also be specified.
+# If `options.sourceMap` is specified, then `options.filename` must also be specified.  See
+# `generateV3SourceMapOptions()` for other options that can be passed to control source map
+# generation.
 #
 # This returns a javascript string, unless `options.sourceMap` is passed,
 # in which case this returns a `{js, v3SourceMap, sourceMap}
@@ -43,8 +75,6 @@ exports.compile = compile = (code, options = {}) ->
   try
 
     if options.sourceMap
-      coffeeFile = helpers.baseFileName options.filename
-      jsFile = helpers.baseFileName(options.filename, yes) + ".js"
       sourceMap = new sourcemap.SourceMap()
 
     fragments = (parser.parse lexer.tokenize(code, options)).compileToFragments options
@@ -80,7 +110,8 @@ exports.compile = compile = (code, options = {}) ->
     answer = {js}
     if sourceMap
       answer.sourceMap = sourceMap
-      answer.v3SourceMap = sourcemap.generateV3SourceMap sourceMap, coffeeFile, jsFile
+      v3Options = generateV3SourceMapOptions options
+      answer.v3SourceMap = sourcemap.generateV3SourceMap(sourceMap, v3Options)
     answer
   else
     js
diff --git a/src/command.coffee b/src/command.coffee
index e33dcbb4..48860469 100644
--- a/src/command.coffee
+++ b/src/command.coffee
@@ -112,9 +112,9 @@ compilePath = (source, topLevel, base) ->
 # Compile a single source script, containing the given code, according to the
 # requested options. If evaluating the script directly sets `__filename`,
 # `__dirname` and `module.filename` to be correct relative to the script's path.
-compileScript = (file, input, base) ->
+compileScript = (file, input, base=null) ->
   o = opts
-  options = compileOptions file
+  options = compileOptions file, base
   try
     t = task = {file, input, options}
     CoffeeScript.emit 'compile', task
@@ -136,7 +136,7 @@ compileScript = (file, input, base) ->
       if o.print
         printLine t.output.trim()
       else if o.compile || o.map
-        writeJs base, t.file, t.output, t.sourceMap
+        writeJs base, t.file, t.output, options.jsPath, t.sourceMap
       else if o.lint
         lint t.file, t.output
   catch err
@@ -264,8 +264,7 @@ outputPath = (source, base, extension=".js") ->
 #
 # If `generatedSourceMap` is provided, this will write a `.map` file into the
 # same directory as the `.js` file.
-writeJs = (base, sourcePath, js, generatedSourceMap = null) ->
-  jsPath = outputPath sourcePath, base
+writeJs = (base, sourcePath, js, jsPath, generatedSourceMap = null) ->
   sourceMapPath = outputPath sourcePath, base, ".map"
   jsDir  = path.dirname jsPath
   compile = ->
@@ -323,15 +322,19 @@ parseOptions = ->
   return
 
 # The compile-time options to pass to the CoffeeScript compiler.
-compileOptions = (filename) ->
+compileOptions = (filename, base) ->
   {
     filename
     literate: helpers.isLiterate(filename)
     bare: opts.bare
     header: opts.compile
     sourceMap: opts.map
+    jsPath: if (filename isnt null and base isnt null) then (outputPath filename, base) else null
+    workingDirectory: process.cwd()
   }
 
+
+
 # Start up a new Node.js instance with the arguments in `--nodejs` passed to
 # the `node` binary, preserving the other options.
 forkNode = ->
diff --git a/src/helpers.coffee b/src/helpers.coffee
index 6e700d7b..03bde1ba 100644
--- a/src/helpers.coffee
+++ b/src/helpers.coffee
@@ -11,6 +11,16 @@ exports.ends = (string, literal, back) ->
   len = literal.length
   literal is string.substr string.length - len - (back or 0), len
 
+# Repeat a string `n` times.
+exports.repeat = repeat = (str, n) ->
+  # Use clever algorithm to have O(log(n)) string concatenation operations.
+  res = ''
+  while n > 0
+    res += str if n & 1
+    n >>>= 1
+    str += str
+  res
+
 # Trim out all falsy values from an array.
 exports.compact = (array) ->
   item for item in array when item
@@ -53,7 +63,7 @@ exports.del = (obj, key) ->
   val
 
 # Gets the last item of an array(-like) object.
-exports.last = (array, back) -> array[array.length - (back or 0) - 1]
+exports.last = last = (array, back) -> array[array.length - (back or 0) - 1]
 
 # Typical Array::some
 exports.some = Array::some ? (fn) ->
@@ -120,3 +130,57 @@ exports.isCoffee = (file) -> /\.((lit)?coffee|coffee\.md)$/.test file
 exports.isLiterate = (file) -> /\.(litcoffee|coffee\.md)$/.test file
 
 
+# Remove any "." components in a path, any ".."s in the middle of a path.  Leaves a trailing '/'
+# if present, unless removeTrailingSlash is set.
+exports.normalizePath = normalizePath = (path, removeTrailingSlash=no) ->
+  root = no # Does this path start with the root?
+  parts = path.split '/'
+  newParts = []
+  i = 0
+  # If the path started with a '/', set the root flag.
+  if parts.length > 1 and parts[0] == ''
+    parts.shift()
+    root = yes
+  for part, i in parts
+    if part in ['.', '']
+      if (i is parts.length - 1) and not removeTrailingSlash
+        # Leave the trailing '/'.  Note that we're pushing a '', but because we join with '/'s
+        # later, this will become a '/'.
+        newParts.push ''
+    else if part is '..'
+      if newParts.length is 0 or (newParts.length and last newParts is '..')
+        # Leave the ".."
+        newParts.push '..'
+      else
+        # Drop the '..' and remote the previous element
+        newParts.pop()
+    else
+      newParts.push part
+  if root
+    if newParts.length is 0 then return '/'
+    if newParts.length[0] is '..'
+      # Uhh...  This doesn't make any sense.
+      throw new Error "Invalid path: #{path}"
+    newParts.unshift '' # Add back the leading "/"
+  newParts.join '/'
+
+# Solve the relative path from `from` to `to`.
+#
+# This is the same as node's `path.relative()`, but can be used even if we're not running in node.
+# If paths are relative (don't have a leading '/') then we assume they are both relative to to
+# same working directory.
+#
+# If `from` is a relative path that starts with '..', then `cwd` must be provided to resolve
+# parent path names.
+exports.relativePath = (from, to, cwd=null) ->
+  if cwd
+    from = cwd + "/" + from
+    to = cwd + "/" + to
+  from = normalizePath(from).split '/'
+  to = normalizePath(to).split '/'
+  while from.length > 0 and to.length > 0 and from[0] == to[0]
+    from.shift()
+    to.shift()
+  if from.length and from[0] is ".." then throw new Error "'cwd' must be specified if 'from' references parent directory: #{from.join '/'} -> #{to.join '/'}"
+  answer = repeat "../", from.length - 1
+  answer + "#{to.join '/'}"
diff --git a/src/sourcemap.coffee b/src/sourcemap.coffee
index 52614b26..bf0d3bbf 100644
--- a/src/sourcemap.coffee
+++ b/src/sourcemap.coffee
@@ -92,7 +92,11 @@ class exports.SourceMap
 # Builds a V3 source map from a SourceMap object.
 # Returns the generated JSON as a string.
 
-exports.generateV3SourceMap = (sourceMap, sourceFile=null, generatedFile=null) ->
+exports.generateV3SourceMap = (sourceMap, options={}) ->
+  sourceRoot = options.sourceRoot or ""
+  sourceFile = options.sourceFile or null
+  generatedFile = options.generatedFile or null
+
   writingGeneratedLine = 0
   lastGeneratedColumnWritten = 0
   lastSourceLineWritten = 0
@@ -146,7 +150,7 @@ exports.generateV3SourceMap = (sourceMap, sourceFile=null, generatedFile=null) -
   answer = {
     version: 3
     file: generatedFile
-    sourceRoot: ""
+    sourceRoot
     sources: if sourceFile then [sourceFile] else []
     names: []
     mappings
diff --git a/test/helpers.coffee b/test/helpers.coffee
index 1644c565..079300eb 100644
--- a/test/helpers.coffee
+++ b/test/helpers.coffee
@@ -2,7 +2,7 @@
 # -------
 
 # pull the helpers from `CoffeeScript.helpers` into local variables
-{starts, ends, compact, count, merge, extend, flatten, del, last, baseFileName} = CoffeeScript.helpers
+{starts, ends, compact, count, merge, extend, flatten, del, last, baseFileName, normalizePath, relativePath} = CoffeeScript.helpers
 
 
 # `starts`
@@ -126,3 +126,48 @@ test "the `baseFileName` helper returns the file name to write to", ->
     filename = name + ext
     eq filename, expectedFileName
 
+
+# `normalizePath`
+
+test "various tests for normalizePath", ->
+  eq "/", normalizePath "/"
+  eq "", normalizePath "."
+  eq "", normalizePath ""
+  eq "/a/b", normalizePath "/a/b"
+  eq "/a/c/", normalizePath "/a/c/"
+  eq "/a/c", normalizePath "/a/c/", true
+  eq "/a/d", normalizePath "/a/../a/./d/c/.."
+  eq "/a/e/", normalizePath "/a/../a/./e/c/../"
+  eq "/a/e", normalizePath "/a/../a/./e/c/../", true
+  eq "../a", normalizePath "../a"
+  eq "../b", normalizePath "a/../../b"
+
+# `relativePath`
+
+test "various tests for relativePath", ->
+  # Same level
+  eq "foo.js", relativePath "foo.coffee", "foo.js"
+  eq "foo.js", relativePath "foo.coffee", "foo.js", "/work/src"
+  # Same level, but both down one level
+  eq "bar.js", relativePath "src/bar.coffee", "src/bar.js"
+  eq "bar.js", relativePath "src/bar.coffee", "src/bar.js", "/work/src"
+  # Sam level, using '.'' as from
+  eq "baz.js", relativePath ".", "baz.js"
+  eq "baz.js", relativePath ".", "baz.js", "/work/src"
+  eq "o/qux.js", relativePath ".", "o/qux.js"
+  eq "o/qux.js", relativePath ".", "o/qux.js", "/work/src"
+  # Up one level
+  eq "../", relativePath "src/bar.js", "."
+  eq "../", relativePath "src/bar.js", ".", "/work/src"
+  # Up and over one directory
+  eq "../dest/foo.js", relativePath "src/foo.coffee", "dest/foo.js"
+  eq "../dest/foo.js", relativePath "src/foo.coffee", "dest/foo.js", "/work/src"
+  # Absolute paths
+  eq "dest1/dest2/bar.js", relativePath "/bar.coffee", "/dest1/dest2/bar.js"
+  # File vs. directory - keep trailing '/'
+  eq "../c", relativePath "a/b/", "a/c"
+  eq "../d/", relativePath "a/b/", "a/d/"
+  # This should throw, since relativePath can't know the name of the directory that foo.coffee is in.
+  throws -> relativePath "../o/foo.js", "foo.coffee"
+  # With the CWD, this should pass.
+  eq "../src/foo.coffee", relativePath "../o/foo.js", "foo.coffee", "/work/src"
diff --git a/test/sourcemap.coffee b/test/sourcemap.coffee
index 2770fb6c..4eede954 100644
--- a/test/sourcemap.coffee
+++ b/test/sourcemap.coffee
@@ -36,7 +36,11 @@ test "SourceMap tests", ->
   map.addMapping [1, 9], [2, 8]
   map.addMapping [3, 0], [3, 4]
 
-  eqJson (sourcemap.generateV3SourceMap map, "source.coffee", "source.js"), '{"version":3,"file":"source.js","sourceRoot":"","sources":["source.coffee"],"names":[],"mappings":"AAAA;;IACK,GAAC,CAAG;IAET"}'
+  testWithFilenames = sourcemap.generateV3SourceMap map, {
+        sourceRoot: "",
+        sourceFile: "source.coffee",
+        generatedFile: "source.js"}
+  eqJson testWithFilenames, '{"version":3,"file":"source.js","sourceRoot":"","sources":["source.coffee"],"names":[],"mappings":"AAAA;;IACK,GAAC,CAAG;IAET"}'
   eqJson (sourcemap.generateV3SourceMap map), '{"version":3,"file":null,"sourceRoot":"","sources":[],"names":[],"mappings":"AAAA;;IACK,GAAC,CAAG;IAET"}'
 
   # Look up a generated column - should get back the original source position.