AIM:To investigate peripapillary retinal nerve fiber layer (RNFL), macula and ganglion cell layer thicknesses (GCC) in amblyopic eyes with spectral domain optical coherence tomography (SD-OCT).METHODS:Thirty six patients with a history of unilateral amblyopia and thirty two children who had emmetropia without amblyopia were included in this study.In this institutional study, 36 eyes of 36 patients with amblyopia (AE), 36 fellow eyes without amblyopia (FE), and 32 eyes of 32 normal subjects (NE) were included. RNFL, GCC and macular thickness measurements were performed with RS-3000 OCT Retina Scan (Nidek Inc CA. USA).RESULTS:The mean global thicknesses of the RNFL were 113.22±21.47, 111.57±18.25, 109.96±11.31μm in the AE, FE, and NE, respectively. There was no statistically significant difference for mean global RNFL thickness among the eyes (P=0.13). The mean thicknesses of the macula were 258.25±18.31, 258.75±19.54, 248.62±10.57μm in the AE, FE and NE, respectively. There was no statistically significant difference for thickness of macula among the eyes (P=0.06). The GCC was investigated into two parts:superior and inferior. The mean thicknesses of superior GCC were 102.57±13.32, 103.32±10.64, 100.52±5.88μm in the AE, FE, and NE, respectively. The mean thicknesses of inferior GCC were 103.82±12.60, 107.82±12.33, 105.86±10.79μm in the AE, FE and NE, respectively. There was no statistically significant difference for thickness of superior and inferior GCC between the eyes (P=0.63, P=0.46).CONCLUSION:The macular thicknesses of AE and FEwere greater than the NE, although it was not statistically significant. Amblyopia does not seem to have a profound effect on the RNFL, macula and GCC.