Deficiencies of vitamin A, iron, and zinc are prevalent worldwide, affecting vulnerable groups such as lactating women and infants. However, the existence of concurrent deficiencies has received little attention. The aim was to investigate the extent to which deficiencies of vitamin A, iron, and zinc coexist and the nutritional relation between lactating mothers and their infants. In a cross-sectional survey in rural West Java, Indonesia, 155 lactating mothers and their healthy infants were assessed anthropometrically and blood, urine, and breast-milk samples were obtained. Marginal vitamin A deficiency was found in 54% of the infants and 18% of the mothers. More than 50% of the mothers and infants were anemic and 17% of the infants and 25% of the mothers were zinc deficient. There was a strong interrelation between the micronutrient status of the mothers and infants and the concentrations of retinol and beta-carotene in breast milk. Vitamin A deficiency in infants led to an increased risk of anemia and zinc deficiency (odds ratios: 2.5 and 2.9, respectively), whereas in mothers the risk of anemia and iron deficiency (odds ratios: 3.8 and 4.8, respectively) increased. In infants, concentrations of insulin-like growth factor I were related to concentrations of plasma retinol and beta-carotene but not to zinc. Micronutrient deficiencies were prevalent in West Java. The micronutrient status of lactating mothers and that of their infants were closely related; breast milk was a key connecting factor for vitamin A status. Furthermore, concurrent micronutrient deficiencies appeared to be the norm.