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Vitamin D has a role in both insulin secretion and insulin sensitivity, and thus could be important in the pathogenesis of diabetes. The aim of this study was to compare the effect of yogurt fortified with vitamin D and oral vitamin D supplement on glycemic and anthropometric indices in pre-diabetic individuals. This study was conducted on 90 subjects with pre-diabetes in three groups: those given fortified yogurt with vitamin D, those given plain yogurt and those given oral vitamin D supplements. The study variables were evaluated at the beginning and end of the intervention period. Results from the participants’ oral glucose tolerance tests (OGTT) decreased significantly in only the fortified-yogurt group. The mean fasting serum insulin and the insulin-resistance index (HOMA-IR) in the fortified-yogurt (p < .01) and oral-supplement (p < .03, p < .04) groups decreased significantly. Waist-to-hip ratio (WHR) and percentage of body fat (PBF) decreased significantly in the fortified-yogurt (p < .02, p < .006) and oral-supplement (p = .015, p < .001) groups. These findings show that yogurt fortified with vitamin D improves glycemic and anthropometric indices in pre-diabetic individuals.