diff --git a/lib/contracts/compiler.js b/lib/contracts/compiler.js
index 450067da..15f13b16 100644
--- a/lib/contracts/compiler.js
+++ b/lib/contracts/compiler.js
@@ -7,6 +7,7 @@ class Compiler {
     this.plugins = options.plugins;
     this.logger = options.logger;
     this.solcVersion = options.solcVersion;
+    this.contractDirectories = options.contractDirectories;
   }
 
   compile_contracts(contractFiles, cb) {
@@ -56,7 +57,12 @@ class Compiler {
       function prepareInput(callback) {
         async.each(contractFiles,
                    function(file, fileCb) {
-                     let filename = file.filename.replace('app/contracts/', '');
+                     let filename = file.filename;
+
+                     for (let directory of self.contractDirectories) {
+                       filename = filename.replace(directory, '');
+                     }
+
                      file.content(function(fileContent) {
                       input[filename] = fileContent;
                       fileCb();
diff --git a/lib/contracts/contracts.js b/lib/contracts/contracts.js
index 559fa327..8c7616f4 100644
--- a/lib/contracts/contracts.js
+++ b/lib/contracts/contracts.js
@@ -8,6 +8,7 @@ let Compiler = require('./compiler.js');
 class ContractsManager {
   constructor(options) {
     this.contractFiles = options.contractFiles;
+    this.contractDirectories = options.contractDirectories;
     this.contractsConfig = options.contractsConfig;
     this.contracts = {};
     this.logger = options.logger;
@@ -25,7 +26,7 @@ class ContractsManager {
     let self = this;
     async.waterfall([
       function compileContracts(callback) {
-        let compiler = new Compiler({plugins: self.plugins, logger: self.logger, solcVersion: self.solcVersion});
+        let compiler = new Compiler({plugins: self.plugins, logger: self.logger, solcVersion: self.solcVersion, contractDirectories: self.contractDirectories});
         compiler.compile_contracts(self.contractFiles, function (err, compiledObject) {
           self.compiledContracts = compiledObject;
           callback(err);
diff --git a/lib/contracts/deploy_manager.js b/lib/contracts/deploy_manager.js
index 975abae0..9614af1f 100644
--- a/lib/contracts/deploy_manager.js
+++ b/lib/contracts/deploy_manager.js
@@ -26,6 +26,7 @@ class DeployManager {
       function buildContracts(callback) {
         let contractsManager = new ContractsManager({
           contractFiles: self.config.contractsFiles,
+          contractDirectories: self.config.contractDirectories,
           contractsConfig: self.config.contractsConfig,
           logger: self.logger,
           plugins: self.plugins
diff --git a/lib/core/config.js b/lib/core/config.js
index 53825ea4..fc7c2847 100644
--- a/lib/core/config.js
+++ b/lib/core/config.js
@@ -198,6 +198,12 @@ Config.prototype.loadWebServerConfigFile = function() {
 Config.prototype.loadEmbarkConfigFile = function() {
   var contracts = this.embarkConfig.contracts;
   this.contractsFiles = this.loadFiles(contracts);
+  // determine contract 'root' directories
+  this.contractDirectories = contracts.map((dir) => {
+    return dir.split("**")[0];
+  }).map((dir) => {
+    return dir.split("*.")[0];
+  });
 
   this.buildDir  = this.embarkConfig.buildDir;
   this.configDir = this.embarkConfig.config;