Does it need to be stored in the fridge?

A recipe something like this one:

http://sallysbakingaddiction.com/2013/08/06/cookie-dough-pretzel-bites/

I know it says store in the fridge, but I don't know whether that's for the sake of the dough, or the chocolate.

It probably needs to stay refrigerated  because it isn't baked.  It will probably get really soft if left a room temp for a long time.

I don't think it's because of the chocolate.  If you are going to make them, leave one out and see what happens, it will just get soft I bet and then the pretzel will get soft too.

Hope that helps.

I would probably leave them refrigerated until you're ready to serve them. If you're making them and taking them to a party, I would keep them refrigerated until you're ready to leave. I agree with MsGF. I think the dough will get really soft like regular cookie dough does when left out.