Variations of integral navigation controls may be used in conjunction with a medical instrument to provide navigation functions for an image guided surgery (IGS) system that is in communication with the integral navigation controls. In some variations, a medical instrument with integrated navigation wheels allows movement of a cursor of the IGS system along the x and y axis by scrolling the wheel, or allows selection, zooming, or other controls by combined clicking and/or scrolling of wheels, and may be sterilized or discarded along with the device. In some other variations, a control overlay may be temporarily attached to the medical instrument to provide additional controls, such as buttons or a pointing stick, and then removed and sterilized or discarded after a procedure. In each variation, inputs may be communicated via wire or wirelessly to an IGS system to provide navigation of images during a surgical procedure.