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Maternal vitamin D may be important for several organ systems in the offspring, including the reproductive system. In this population-based follow-up study of 12,991 Danish boys and girls born 2000–2003, we investigated if maternal intake of vitamin D supplements during pregnancy was associated with pubertal timing in boys and girls. Information on maternal intake of vitamin D supplements was obtained by self-report in mid-pregnancy. Self-reported information on the current status of various pubertal milestones was obtained every six months throughout puberty. Mean differences in months at attaining each pubertal milestone and an average estimate for the mean difference in attaining all pubertal milestones were estimated according to maternal intake of vitamin D supplements using multivariable interval-censored regression models. Lower maternal intake of vitamin D supplements was associated with later pubertal timing in boys. For the average estimate, boys had 0.5 months (95% CI 0.1; 0.9) later pubertal timing per 5 µg/day lower maternal vitamin D supplement intake. Maternal intake of vitamin D supplements was not associated with pubertal timing in girls. Spline plots and sensitivity analyses supported the findings. Whether the observed association with boys’ pubertal timing translates into an increased risk of disease in adulthood is unknown.