The efficacy of the Shack-Hartmann technique for measuring the optical aberrations of the eye was evaluated for four classes of clinical conditions associated with optically abnormal eyes. These categories (with specific examples) are: anomalies of the tear film (dry eye), corneal disease (keratoconus), corneal refractive surgery [laser-assisted in situ keratomileusis (LASIK)], and lenticular cataract. We show that in each of these cases, it is possible to obtain at least a partial topographic map of the refractive aberrations of the patient's eyes, but severe losses of data integrity can occur. We further show that the Shack-Hartmann aberrometer provides additional information about the eye's imperfections on a very fine spatial scale (< 0.4 mm) which scatter light and further degrade the quality of the retinal image. Taken together, spatial maps of the variation of optical aberrations and scatter across the eye's entrance pupil represents an improved description of the optical imperfections of the abnormal eye.