The aim of this study was to assess the relationship between obesity and vitamin D status cross-sectionally, the relationship between obesity and the incidence of hypovitaminosis D prospectively and inversely the relationship between vitamin D status and incidence of obesity in a population-based cohort study in Spain. At baseline (1996-1998), 1226 subjects were evaluated and follow-up assessments were performed in 2002-2004 and 2005-2007, participants undergoing an interview and clinical examination with an oral glucose tolerance test. At the second visit, 25-hydroxyvitamin D and intact parathyroid hormone concentrations were also measured. Prevalence of obesity at the three visits was 28.1, 36.2 and 39.5%, respectively. The prevalence of vitamin D deficiency (25-hydroxyvitamin D ≤ 20 ng/ml (≤ 50 nmol/l)) was 34.7%. Neither obesity at baseline (OR=0.98, 95% CI: 0.69-1.40, P=0.93) nor the development of obesity between baseline and the second evaluation (OR=0.80, 95% CI: 0.48-1.33, P=0.39) were significantly associated with vitamin D status. In subjects who were non-obese (BMI <30 kg/m²) at the second evaluation, 25-hydroxyvitamin D values ≤ 17 ng/ml (≤ 42.5 nmol/l) were significantly associated with an increased risk of developing obesity in the next 4 years (OR=2.35, 95% CI: 1.03-5.4, P=0.040 after diverse adjustments). We conclude that vitamin D deficiency is associated with an increased risk of developing obesity.