In a laser cataract procedure that also corrects for astigmatism, an iris registration method compares an iris image of a patient's eye taken when the eye is not docked to a patient interface device with an iris image of the same eye that is docked to the patient interface, to calculate a rotation angle between the two images. The astigmatism axis of the eye is measured when the eye is not docked, and the measured axis is rotated by the calculated rotation angle to obtain a rotated astigmatism axis relative to the iris image of the docked eye. The laser cataract procedure is performed based on the rotated astigmatism axis. The rotation angle is calculated by optimizing a transformation that transforms the undocked iris image to match the docked iris image, where the transformation includes a dilation factor that accounts for different pupil dilation of the two iris images.