diff --git a/lib/core.js b/lib/core.js
index 5fa0bff7..2bb69fc6 100644
--- a/lib/core.js
+++ b/lib/core.js
@@ -174,7 +174,7 @@ SystemJSLoader.prototype.config = function(cfg) {
       for (var p in obj)
         return true;
     }
-    if (checkHasConfig(this.packages) || checkHasConfig(this.meta) || checkHasConfig(this.depCache) || checkHasConfig(this.bundles))
+    if (checkHasConfig(this.packages) || checkHasConfig(this.meta) || checkHasConfig(this.depCache) || checkHasConfig(this.bundles) || checkHasConfig(this.packageConfigPaths))
       throw new TypeError('baseURL should only be configured once and must be configured first.');
 
     this.baseURL = cfg.baseURL;