PurposeTo use highly precise spectral-domain optical coherence tomography (SD-OCT) to determine whether there were structural abnormalities in the layers of different regions of the fovea in children with anisometropic amblyopia.MethodsEighteen children (mean age 7.8 years old; range 5–11 years) with unilateral anisometropic amblyopia and 18 age-matched control subjects participated. Foveal thickness was measured with an enhanced depth imaging system, SD-OCT and segmented into layers using custom developed software. The thickness of each layer of the fovea was compared among amblyopic eyes, fellow eyes and control eyes with optical magnification correction for axial length and statistical correction for age and sex.ResultsThe total thickness and each intra-ocular layer of the central fovea were the same for each group. However, the amblyopic eyes were significantly thicker than the normal control eyes in 2 of 4 quadrants of the peripheral retina. Exploring intra-retinal layers in these two quadrants, the nasal nerve fiber layer (NFL) and inferior inner nuclear layer (INL)were significantly thicker in amblyopic eyes than in control eyes (p = 0.01 and 0.012, respectively, by ANCOVA).ConclusionThe SD-OCT data revealed marginal differences in some foveal layers at peripheral locations and indicated that structural differences might exist between individuals with amblyopia and visually normal control subjects. However, the differences were scattered and represented no identifiable pattern. More studies with large samples and precise locations of the retinal layers must be performed to extend the present results.