Vitamin A and D serum concentrations and risk factors for their deficiencies were investigated in children participating in a government-sponsored fortified milk program. The study used multivariate linear regression analysis with hierarchical selection of independent variables: socio-demographic conditions, children's health, food consumption, breastfeeding, fortified milk, exposure to sunlight, anthropometric measurements, and serum concentration of retinol and 25(OH)D. Vitamin A and vitamin D insufficiency and deficiency values were defined as < 1.05 µmol/L, < 0.7 µmol/L, < 30 ng/mL, and < 20 ng/mL, respectively. Vitamin A and D intake was inadequate. Prevalence rates for vitamin A and vitamin D insufficiency and deficiency were 19%, 6%, 82%, and 58%, respectively. Factors associated with low serum vitamin A were exclusive breastfeeding for less than 120 days, low maternal schooling, maternal unemployment, more consumers of fortified milk in the family, and low serum vitamin D. Factors associated with vitamin D deficiency were low exposure to sunlight and low serum vitamin A. Nutritional education is needed to improve children's nutritional status.