Have you checked where they are connected to and if they are connected firmly? If one is CPU (processor) fan be sure to connect it to the 4-pin plug on your motherboard labelled CPU FAN, it can also be a three pin plug. If it's just a chassis fan, as pdxalex said, try the molex connectors (the 4 pin plug coming through a wire straight from the power supply). Otherwise, spare 3-pin or 4-pin plugs can be used. Whatever you do, don't leave your processor fan unplugged, and try not to unplug it in the first place.
Hope this helped