Objective: To compare central macular and retinal nerve fiber layer (RNFL) thickness using Spectral Domain Optical Coherence Tomography (SD-OCT) among patients with hyperopic anisometropic, strabismic and mixed amblyopia and healthy controls.Method: This prospective, cross-sectional study included 39 amblyopic children, their fellow eyes and 20 healthy individuals. Central macular and RNFL (superior, nasal, inferior and temporal quadrants and mean RNFL) thicknesses were measured with SD-OCT.Results: Difference was not statistically significant in the central macular thickness when the anisometropic, strabismic and mixed amblyopia groups were compared among themselves, fellow eyes and healthy control group.In the anisometropic amblyopic group, the inferior RNFL and nasal RNFL values were significantly thicker compared to the fellow eyes (p=0.009, p=0.028, respectively). Mean RNFL measurements were significantly thicker in anisometropic and mixed groups in the amblyopic eyes compared to the fellow eyes (p=0.009, p=0.031, respectively). In the temporal quadrant, the RNFL was found to be statistically significantly thinner in the anisometropic and mixed amblyopic groups compared to the fellow eyes (p=0.049, p=0.010, respectively).Conclusions: There was no considerably difference in the central macular thickness among the amblyopia groups, fellow eyes and healthy controls. However, significant changes were found in the mean RNFL and certain quadrants of the RNFL thicknesses in the anisometropic and mixed amblyopic groups.