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Vitamin D insufficiency and deficiency are prevalent worldwide, with the highest prevalence in the northern countries due to the lack of ultraviolet exposure. The individual effect of vitamin D on bone mineral density (BMD) has been studied but the results are inconclusive.The aim of our study was to investigate the effect of vitamin D on BMD in a random population-based cohort of Estonian adults.A cross-sectional population-based study. A total of 273 individuals free of diseases or states known to affect bone or vitamin D metabolism participated in the study. We measured BMD, vitamin D and parathyroid hormone concentrations (in winter and in summer). Several co-variables were included in the regression analysis, including age, smoking, alcohol consumption, body mass index, physical activity, fresh milk consumption, caffeinated beverage consumption, lean tissue mass and total body fat percentage, and in women the number of children and breastfeeding history.We show that summer vitamin D independently correlates with BMD in lumbar spine, trochanter and total body regions (P < 0.05 to 0.01). Subgroup analysis for women showed that summer vitamin D predicts independently lumbar spine (P < 0.05) and in men total body BMD (P < 0.01). Lean tissue mass and fat mass were additional contributors of the BMD (P < 0.001).In addition to body composition indices, vitamin D could be an independent contributor of BMD in several skeletal regions in men and women.