To determine the choroidal thickness (mainly subfoveal) using spectral domain optical coherence tomography (SD-OCT) in amblyopic eyes and to compare it with the choroidal thickness (CT) of healthy fellow eyes. In this prospective study, 140 eyes of 70 patients (aged 5-40 years) with strabismic and anisometropic amblyopia were examined using enhanced depth imaging (EDI) mode in SD-OCT. The CT was measured directly below the fovea and six other locations: 500 μ, 1000 μ, and 1500 μ from fovea in both nasal and temporal quadrants. The mean age of the patients was 22.5 ± 11.2 years. The mean Best Corrected Visual Acuity (BCVA) in the amblyopic eyes was 0.87 ± 0.47 logMAR and 0 ± 0.02 logMAR in control eyes. The average subfoveal CT was 341.73 ± 60.39 μm in the amblyopic eyes and 314.77 ± 48.12 μm in the fellow eyes. Subgroup analysis showed that the patients with anisometropic amblyopia had a significantly thicker choroid as compared to the fellow healthy eyes (P = 0.00), whereas in strabismic amblyopic eyes, this difference was not significantly significant (P = 0.064). Significant choroidal thickening was observed in subjects with amblyopia, which may contribute to the amblyopia pathogenesis and this could be used as a diagnostic parameter for amblyopia. These changes were more pronounced in patients with anisometropic amblyopia than strabismic amblyopia.