Background and Objectives: The aim of the study is to assess macular ganglion cell and inner plexiform layer (mGCIPL) thickness in deprivational amblyopic eyes (AE), fellow non-amblyopic eyes (FE) and normal eyes (NE) using spectral. domain optical coherence tomography (SD-OCT). Materials and Methods: Twenty two children (64% boys) who underwent surgical removal of unilateral congenital or developmental cataracts and exhibited visual impairment despite postoperative visual rehabilitation were included in the study. Cataract surgery was performed in patients aged 55.82 ± 35.85 months (range 6 to 114 months). The mean age of the study group was 9.73 ± 2.85 years (range 5 to 15 years). The comparison group consisted of 22 healthy age- and gender-matched children. The best corrected visual acuity (BCVA) after surgery was: 0.75 ± 0.27 (range 0.3 to 1.3) in AE, 0.1 ± 0.13 (range 0 to 0.5) in FE and 0.04 ± 0.07 (range 0 to 0.2) in NE. OCT scans were performed in all patients and subsequently corrected for axial length related magnification errors. Results: The average thickness of mGCIPL was 70.6 ± 11.28 μm in AE; 77.50 ± 6.72 μm in FE and 81.73 ± 5.18 μm in NE. We found that mGCIPL was statistically significantly thinner in deprivation AE compared to FE (p = 0.038) and NE (p = 0.0005). The minimum thickness of mGCIPL was respectively: 62.68 ± 13.2 μm, 70.3 ± 7.61 μm, and 74.5 ± 5.47, and also differed between AE and FE (p = 0.023) and AE and NE (p = 0.0004). Also, measurements in the inferior, inferotemporal, and superotemporal sectors showed thinning of mGCIPL in AE compared to NE. Conclusions: This analysis may suggest that deprivational amblyopia caused by unilateral congenital or developmental cataract in children may be associated with mGCIPL thinning.