The aim of this study was to investigate the presence of increased macular or retinal nerve fiber layer thickness (RNFLT) in amblyopic eyes, find if the increased macular or RNFLT is related to the lack of response in amblyopic eyes, and to explore whether the increased central macular thickness (CMT) in amblyopic eyes is purely related to the hyperopia. This is a prospective descriptive study. CMT and peripapillary RNFLT were measured by spectral-domain optical coherence tomography to evaluate 60 patients with unilateral-treated amblyopia (median age 11.00 year). Patients were divided into two groups: 33 patients in recovered amblyopia group and 27 patients in persistent amblyopia group. The mean CMT in the recovered group was 247.31 (±23.4) versus 246.8 (±32.7) µm (p = 0.95) for the persistent group. The mean peripapillary RNFLT was 99.13 (±12.1) versus 99.9 (±14.9) µm (p = 0.85) for the persistent group. In anisometropic amblyopia, there was no significant difference in CMT and RNFLT in either group. Also there was no relation between the type of refractive error and CMT or RNFLT. There was no significant difference in CMT and RNFLT in amblyopic eyes for both the recovered amblyopia group and the persistent amblyopia group to explain the lack of response in persistent amblyopic eyes. Additionally there was no relation between the type of refractive error and CMT or peripapillary RNFLT.