The authors compared the macular and peripapillary retinal nerve fibre layer (RNFL) thicknesses of amblyopic and fellow eyes using Stratus optical coherence tomography (OCT) to reveal any differences. They sought to determine the anatomical differences between these subtypes of strabismic and anisometropic amblyopia. They recruited 25 strabismic (22 esotropia and three exotropia) and 25 anisometropic (21 anisohyperopic and four anisomyopic) subjects. In the anisometropic group macular thickness of amblyopic eyes was significantly greater than the fellow eye. No significant difference in RNFL thickness was found for this group. In the strabismic group, no significant difference between eyes was found either for macular or RNFL thickness.