I've seen several posts explain how to set the assembly version programmatically, although I can't remember how to do it exactly. It would involve a VS macro or some other form of VS extension I would assume. Note also that Setup projects allow you to specify prebuild actions, one of which could be incrmenting the version number, while ClickOnce publishing doesn't as far as I'm aware. That means that you'd have to invoke your macro manually from the tool bar or menu system before publishing.