Retinal imaging with an adaptive optics system usually requires that the eye be centered and stable relative to the exit pupil of the system. Aberrations are then typically corrected inside a fixed circular pupil. This approach can be restrictive when imaging some subjects since the pupil may not be round and maintaining a stable head position can be difficult. In this paper we present an automatic algorithm that relaxes these constraints. An image quality metric is computed for each spot of the Shack Hartmann image to detect the pupil and its boundary and the control algorithm is applied only to regions within the subject’s pupil. Images on a model eye as well as for five subjects were obtained to show that a system exit pupil larger than the subject’s eye pupil could be used for AO retinal imaging without a reduction in image quality. This algorithm automates the task of selecting pupil size. It also may relax constrains on centering the subject’s pupil and on the shape of the pupil.