OBJECTIVE To evaluate the peripapillary choroidal thickness (CT) in children with unilateral amblyopia using spectral-domain optical coherence tomography (SD-OCT). METHODS One hundred and six eyes of 53 children with unilateral amblyopia and 20 eyes of 20 children with normal vision were involved in this study. Of the 53 children with unilateral amblyopia, 29 (54.7%) had hyperopic anisometropic amblyopia and 24 (45.3%) had strabismic amblyopia. Peripapillary CT was measured from 6 mm length radial B-scans at the optic nerve head using the enhanced depth imaging program of an SD-OCT (Heidelberg Engineering, Germany). Age, sex, refractive error, and best-corrected visual acuity were also recorded. RESULTS The average peripapillary CT was greater in amblyopic eyes than in the fellow eyes of the children with amblyopia (P = 0.002), and control eyes (P < 0.001). There was no significant difference between the fellow eyes of children with amblyopia and the control eyes (P = 0.158). The average peripapillary CT was negatively correlated with axial length (AL) in amblyopic eyes (r = -0.381; P = 0.005) and fellow eyes (r = -0.392; P = 0.004) but not in control eyes (r = -0.232; P = 0.325). After adjustment for the possible effects of AL, the average peripapillary CT in amblyopic eyes was still greater than in fellow eyes (P = 0.014) and control eyes (P = 0.022). CONCLUSIONS The peripapillary choroid of eyes with amblyopia was thicker than that of the fellow eyes and control eyes. No significant difference was observed between fellow eyes and control eyes.