The present study was conducted to investigate the effect of vitamin D Mega-dose supplementation on various aspects of physical and mental health of adolescent girls in Mashhad and Sabzevar Cities. The study population included 988 adolescent girls that took 9 Pearls of vitamin D during 9 weeks. Each tablet contains 50000IU vitamin D. inclusion criterion included adolescent girls with age of between 12 to 18 years; also exclusion criteria included history of chronic diseases, cancer or using of drugs and supplements. Samples of fasting blood, urine and stool were taken in the morning at baseline and after one week of 9 weeks intervention. Validated questionnaires are used for assessment of other variables. serum levels of vitamin D, inflammatory markers, blood glucose, lipid profile, liver and kidney function tests, demographic information, medical history status, sun exposure, use of sunscreen, anthropometric factors, gastrointestinal micro biome, dietary intakes and dietary patterns, dietary habits, physical activity, sleep disorders, Cognitive abilities, quality of life, feel of pain, blood pressure, depression and aggression, irritable bowel syndrome, menstrual disorder and polymorphisms of genes related to vitamin D were assessed before and after of vitamin D supplementations. The ethical committee of Mashhad University of Medical Sciences approved the study, and informed written consent was obtained from all participants.