Purpose: To compare the macular and peripapillary RNFL thicknesses of the amblyopic and normal eye in patients with anisometropic amblyopia. Methods: This is a hospital based cross-sectional study for which we studied 36 amblyopic subjects aged between 5 to 16 years in which the amblyopic eye was taken as the case and the unaffected eye was taken as control eye. The inclusion criteria included children having unilateral strabismic or anisometropic amblyopia who underwent macular and RNFL thickness assessment by SD-OCT. Results: Central Macular thickness as well as the thickness of the other macular segments was significantly greater in the affected eye (p<0.001) as compared to the normal eye. The average RNFL thickness was also found to be increased in the affected eye but the difference was not statistically significant (p=0.106), however it was statistically significant in quadrantic analysis (p<0.05). The Central Macular thickness showed a negative correlation with the BCVA (r=- 0.252), although it was not statistically significant (p=0.139). Conclusion: A significant increase was found in the macular as well as RNFL thickness in the amblyopic eyes as compared to the normal fellow eye which support the hypothesis of decreased apoptosis of the ganglion cells postnatally.