Objectives. In adults, obesity is linked to changes in the retinal microvasculature. Limited research has been conducted into this association in children. We examined in a cohort of pre-adolescents the relationship between body mass index (BMI) and retinal vascular structure, including retinal vessel diameter and retinal vessel fractals, a measure of geometric patterns reflecting vessel density. Methods. A population-based study among school children (2 353/3 144 [75.3%], median age, 12.7 years) recruited from a random cluster sample of 21 schools was conducted during 2004–5. Retinal images were taken and vessel diameter and fractal dimension were quantified using computer-based programs following standardized protocols. Anthropometric measures (weight, height, waist circumference, and BMI) were obtained and defined using standardized protocols. Results. Children with the highest quartile of BMI had narrower retinal arteriolar diameter (2.8 μm narrower, p<0.0001) and wider venular caliber (4.2 μm wider, p=0.001) than those with BMI in the lowest quartile, after adjusting for age, sex, ethnicity, mean arterial blood pressure, iris color, axial length, birth weight and fellow retinal vessel caliber. Obese children had narrower retinal arteriolar diameter (2.8 μm narrower, p=0.01) and wider venular diameter (4.5 μm wider, p=0.01) than in non-overweight/obese children. Retinal fractal dimension was not significantly associated with BMI. Increasing quartiles of waist circumference were also associated with retinal vessel diameter. Conclusions. Our data provide evidence of adverse retinal microvascular caliber changes in obese pre-adolescent children, well before the onset of metabolic and cardiovascular disease in adulthood, and support an early, generalized adverse effect of adiposity on microvascular structure.