AIM: To determine lamina cribrosa thickness (LCT) in the optic nerve head region of the eyes in children with hyperopic anisometropic amblyopia and to compare this thickness with that of fellow eyes, hyperopic non-amblyopia, and age-matched controls. METHODS: Thirty-two patients (12.0±1.8y, mean± standard deviation) with hyperopic anisometropic amblyopia, 31 subjects with age- and refractive error- matched hyperopic non-amblyopia (10.7±2.2y), and 32 age-matched controls (11.2±2.0y) were included in this prospective, cross-sectional study. LCT was measured using an enhanced depth-imaging program of a spectral domain optical coherence tomographic instrument in all participants, and the correlation between LCT and axial length was calculated. RESULTS: The mean LCT was 180.9±29.4 μm in amblyopic eyes, 247.7±19.0 μm in fellow eyes, 251.6±27.3 μm in hyperopic non-amblyopic eyes, and 240.2±15.8 μm in control eyes. Lamina cribrosa in amblyopic eyes was significantly thinner than fellow, hyperopic non-amblyopic, and control eyes (P<0.05). There was no significant correlation in LCT and axial length between amblyopic (P=0.16) and control (P=0.31) group. CONCLUSION: Lamina cribrosa of eyes with hyperopic anisometropic amblyopia is significantly thinner than that of fellow eyes, hyperopic non-amblyopia, and age-matched controls. The LCT profile in amblyopic eyes is different from that observed in fellow, hyperopic non-amblyopic, and control eyes.