Purpose of the Study: The aim of this study was to investigate the presence of gender differences in the chorioretinal microvasculature of children with and without vascular pathology. Methods: Healthy and type 1 diabetic children without diabetic retinopathy underwent optical coherence tomography angiography (OCTA) and structural OCT. We measured the foveal avascular zone (FAZ) area in the superficial capillary plexus (SCP) and deep CP (DCP), central retina, and choroid thickness. Results: OCTA examination was conducted in 112 diabetic and 30 healthy children, and structural OCT in 121 diabetic children and 32 controls. DCP FAZ area in boys was significantly smaller than in girls both in diabetics (p = 0.0010) and healthy children (p = 0.0302). In diabetics, SCP FAZ area was significantly smaller in boys (p = 0.0006), analogically to controls (p = 0.0870). Central retinal thickness was significantly greater in boys compared with girls in diabetics (p = 0.0001) and controls (p = 0.1008). Conclusion: Significant differences exist in the FAZ area and retinal thickness between sexes, likely representing physiological differences. Different norms must be used for boys and girls regardless of diabetic status.