Vitamin D deficiency in pregnancy may be associated with increased offspring adiposity, but evidence from human studies is inconclusive. We examined associations between prenatal vitamin D intake, 25-hydroxyvitamin D (25(OH)D) in cord blood, and offspring size and body composition at birth and 5 months. Participants included 605 mother-offspring dyads from the Healthy Start study, an ongoing, pre-birth prospective cohort study in Denver, Colorado, USA. Prenatal vitamin D intake was assessed with diet recalls and questionnaires, and offspring body composition was measured via air displacement plethysmography at birth and 5 months. General linear univariate models were used for analysis, adjusting for maternal age, race/ethnicity, pre-pregnancy body mass index (BMI), offspring sex, and gestational age at birth. Non-Hispanic white race, lower pre-pregnancy BMI, higher prenatal vitamin D intake, and summer births were associated with higher cord blood 25(OH)D. Higher 25(OH)D was associated with lower birthweight ( = -6.22, = 0.02), but as maternal BMI increased, this association became increasingly positive in direction and magnitude ( = 1.05, = 0.04). Higher 25(OH)D was also associated with lower neonatal adiposity (β = -0.02, p < 0.05) but not after adjustment for maternal BMI ( = -0.01, = 0.25). Cord blood 25(OH)D was not associated with offspring size or body composition at 5 months. Our data confirm the hypothesis that vitamin D exposure in early life is associated with neonatal body size and composition. Future research is needed to understand the implications of these associations as infants grow.