The objective of this study was to evaluate the association of vitamin D intake and serum levels with fracture risk in children under 6 years of age. A case-control study was conducted in Toronto, Ontario, Canada. Cases were recruited from the fracture clinic at the Hospital for Sick Children, and matched controls were obtained from the TARGet Kids! primary-care research network. Controls were matched to cases on age, sex, height, and season. Fracture risk was estimated from conditional logistic regression, with adjustment for skin type, fracture history, waist circumference, outdoor free play, neighborhood income, soda consumption, and child's birth weight. A total of 206 cases were recruited during May 2009-April 2013 and matched to 343 controls. Serum 25-hydroxyvitamin D concentration (per 10-nmol/L increment: adjusted odds ratio (aOR) = 0.95, 95% confidence interval (CI): 0.88, 1.03) and intake of cow's milk (<2 cups/day vs. 2 cups/day: aOR = 0.95 (95% CI: 0.60, 1.52); >2 cups/day vs. 2 cups/day: aOR = 1.39 (95% CI: 0.85, 2.23)) were not significantly associated with reduced odds of fracture. A statistically significant association was observed between child use of vitamin D supplements and decreased odds of fracture (yes vs. no: aOR = 0.42, 95% CI: 0.25, 0.69). Vitamin D supplementation, but not serum 25-hydroxyvitamin D level or milk intake, was associated with reduced fracture risk among these healthy young children.