diff --git a/src/intersectBed/intersectMain.cpp b/src/intersectBed/intersectMain.cpp
index f7524c78beee9e24393c936e724cf3a8876786c1..c26aae0877cac45ba9c139b68dc2db06c63eecac 100644
--- a/src/intersectBed/intersectMain.cpp
+++ b/src/intersectBed/intersectMain.cpp
@@ -217,7 +217,7 @@ int intersect_main(int argc, char* argv[]) {
         showHelp = true;
     }
     
-    if (inputIsBam && writeB) {
+    if (inputIsBam && writeB && outputIsBam) {
         cerr << endl << "*****" << endl << "*****WARNING: -wb is ignored with -abam" << endl << "*****" << endl;
     }