To compare the microstructure and vascularity of amblyopic eyes in children with their contralateral eye and with eyes from control children using optical coherence tomography angiography (OCT-A).We conducted a prospective, cross-sectional evaluation of macular and optic disk vascular density and flow area using OCT-A (Avanti RTVue XR, Optovue Inc, Fremont, CA). Parameters were calculated using automated software.A total of 52 children were included: 26 subjects with amblyopia and 26 nonamblyopic controls. The amblyopic eye of subjects showed a statistically significant decrease in macular vascular density (P = 0.0171) of the superficial capillary plexus (SCP), in the optic disk flow area (P = 0.0195) and in the average retinal nerve fiber layer thickness (P = 0.0194) as well as a marginally statistically significant decrease in the macular flow area of the SCP (P = 0.0305) and in the optic density (P = 0.0279). Compared with randomly selected eyes of controls, amblyopic eyes showed a statistically significant decrease in the macular flow area of the SCP (P = 0.005) and of the deep capillary plexus (DCP; P = 0.002), in the macula vascular density of the SCP (P = 0.022), in the optic disk flow area (P = 0.004), and a marginally statistical significant increase in the area of foveal avascular zone of the DCP (P = 0.038).In our study cohort amblyopic eyes manifested significant differences in macular and optic disk vascularization. The clinical significance of these findings warrants further research.