diff --git a/lib/sandboxed_module.js b/lib/sandboxed_module.js
index 6bf483c..17aeef0 100644
--- a/lib/sandboxed_module.js
+++ b/lib/sandboxed_module.js
@@ -8,6 +8,7 @@ var builtinModules = require('./builtin_modules.json');
 var parent = module.parent;
 var globalOptions = {};
 var registeredBuiltInSourceTransformers = ['coffee'];
+var builtInSourceTransformersConfig = {};
 
 module.exports = SandboxedModule;
 function SandboxedModule() {
@@ -27,7 +28,7 @@ SandboxedModule.load = function(moduleId, options, trace) {
 
   var sandboxedModule = new SandboxedModule();
   sandboxedModule._init(moduleId, trace, options);
-  sandboxedModule._compile()
+  sandboxedModule._compile();
   return sandboxedModule;
 };
 
@@ -42,10 +43,11 @@ SandboxedModule.configure = function(options) {
   });
 };
 
-SandboxedModule.registerBuiltInSourceTransformer = function(name) {
+SandboxedModule.registerBuiltInSourceTransformer = function(name, config) {
   if(registeredBuiltInSourceTransformers.indexOf(name) === -1) {
-    registeredBuiltInSourceTransformers.push(name)
+    registeredBuiltInSourceTransformers.push(name);
   }
+  builtInSourceTransformersConfig[name] = config;
 };
 
 
@@ -308,24 +310,33 @@ function getStartingSourceTransformers() {
 var builtInSourceTransformers = {
   coffee: function(source) {
     if (this.filename.search(/\.coffee$/) !== -1){
-      return require('coffee-script').compile(source);
+      return require('coffee-script').compile(source, builtInSourceTransformersConfig.coffee);
     } else {
       return source;
     }
   },
   istanbul: function(source) {
-    var coverageVariable, istanbulCoverageMayBeRunning = false;
-    Object.keys(global).forEach(function(name) {
-      if((name.indexOf("$$cov_") === 0 || name === '__coverage__') && global[name]) {
-        istanbulCoverageMayBeRunning = true;
-        coverageVariable = name;
-      }
-    });
+    var config = {};
+    if(builtInSourceTransformersConfig.istanbul) {
+      Object.keys(builtInSourceTransformersConfig.istanbul).forEach(function(option) {
+        config[option] = builtInSourceTransformersConfig.istanbul[option];
+      });
+    }
+
+    var istanbulCoverageMayBeRunning = config.coverageVariable && global[config.coverageVariable];
+    if(!istanbulCoverageMayBeRunning) {
+      Object.keys(global).forEach(function(name) {
+        if((name.indexOf("$$cov_") === 0 || name === '__coverage__') && global[name]) {
+          istanbulCoverageMayBeRunning = true;
+          config.coverageVariable = name;
+        }
+      });
+    }
 
     if(istanbulCoverageMayBeRunning) {
       try {
         var istanbul = require('istanbul'),
-            instrumenter = new istanbul.Instrumenter({coverageVariable: coverageVariable}),
+            instrumenter = new istanbul.Instrumenter(config),
             instrumentMethod = instrumenter.instrumentSync.bind(instrumenter);
         source = instrumentMethod(source, this.filename);
       } catch(e) {}