Purpose:To compare macular thickness in children with functional amblyopia and those without amblyopia using optical coherence tomography (OCT).Methods:This case-control study was conducted on 93 children aged 3–10 years including 44 cases with unilateral amblyopia and 49 subjects without amblyopia. Amblyopic eyes were considered as the case group and their fellow eyes as internal controls; eyes of non-amblyopic children served as the external control. Macular thickness of all eyes were measured by optical coherence tomography in the center (foveola), 1 mm ring (fovea), and 3 and 6 mm rings and compared.Results:Although macular thickness was generally not different between the study groups, there was a significant difference in central macular thickness between eyes with moderate to severe amblyopia and the external controls (P = 0.037). Foveal thickness difference exceeding 10 microns between fellow eyes was detected in a larger number of amblyopic children as compared to non-amblyopic controls (P = 0.002). Mean foveal thickness was greater in boys (P = 0.037) but there was no significant difference in foveal thickness among various types of refractive errors.Conclusion:Although there was no significant relationship between macular thickness and amblyopia, foveolar thickness in eyes with moderate to severe amblyopia was significantly greater than the external controls. Further studies with more cases of moderate to severe amblyopia are recommended.