A method and system are provided for sensing the position of a rotor in a hybrid stepper motor. First and second Hall sensors are positioned in a spaced-apart relationship with the first and second armatures of the rotor such that the first and second Hall sensors generate electrical outputs that are 90.degree. out of phase with one another as the rotor rotates. The electrical outputs are adjusted relative to a reference, and the amplitude of the electrical outputs is further adjusted to account for spacing differences between the rotor and each of the first and second Hall sensors
