A wavefront measurement system, for measurement of aberrations in the eye, and for measurement of the topography of the cornea of the eye. The system differs from previously available systems in that the wavefront measurement of the eyes aberrations can be performed as a function of eye accommodation. Furthermore, methods for reducing corneal reflection are described. Additionally, the use of a very short focal length Hartman Shack lenslet array enables a very wide range of low order aberrations, up to ±25 diopters, to be measured without any refocusing or motion of the system. Also, methods are described for enabling the presence of defects within the eye to be determined using the aberration measurement system. Another embodiment captures the pupil centering position without any projected illumination pattern being used, so that a subsequent accurate centering and focusing procedure can commence at the initially captured position, thus reducing measurement time.