diff --git a/lib/compile.js b/lib/compile.js
index e25c0a4..cd6eaee 100644
--- a/lib/compile.js
+++ b/lib/compile.js
@@ -213,13 +213,15 @@ function compileTree(loader, tree, traceOpts, compileOpts, outputOpts, cache) {
       return [];
 
     return Promise.all(compileOpts.entryPoints.map(function(entryPoint) {
-
-      // NB do we need to check that entry points are conditionally unique?
       return loader.normalize(entryPoint)
       .then(function(normalized) {
         return loader.getCanonicalName(normalized);
       });
-    }));
+    }))
+    .filter(function(inputEntryPoint) {
+      // skip conditional entry points
+      return !inputEntryPoint.match(/\#\:|\#\?|\#{/);
+    })
   })
   .then(function(inputEntryPoints) {
     entryPoints = inputEntryPoints || [];