A system and method for aligning a first and a second image of an eye includes making a determination of a limbus location on a first eye image and a second eye image. The limbus location of the first and the second eye images are then aligned in two dimensions. A second eye feature location is determined on the first and the second eye image. One of the first and the second eye image is relatively rotated, and a correlation is performed on the first and the second eye image at a plurality of relative rotational positions using the second eye feature location. From the correlation an optimal first and second image alignment is identified.