What exactly do you mean by home made? You made a complete fan of some kind, or rigged a normal case fan to a usb plug?
The effect it will have on the motherboard depends on what you are doing with it. If you're asking whether plugging it in will fry the board or USB socket, yes it could cause some damage. It depends on what kind of fan it is and how you wired it. If you need to ask about it, then you probably don't have the knowledge needed to attempt something like this and make it work.
Most case fans run on 12 volts while USB operates at 5 volts. Unless you know you have a 5 volt fan from somewhere, and know enough to wire it up correctly, I recommend that you just go buy a fan for your needs.