Background: Children's developing bones depend on vitamin D. Vitamin D is involved in several physiological and pathological processes in addition to maintaining bone integrity and absorbing calcium. The present study was conducted to Prevalence of Vitamin D deficiency and associated risk factors among school children residing at high altitude in Ladakh, India. Materials & Methods: 240 children of both genders were selected. Parameters such as height, weight, Body mass index (BMI) as weight (kg)/height (m2), socio economic status (SES), physical activity, sunlight exposure, and dietary pattern was recorded. The biochemical estimation of serum 25 hydroxy Vitamin D ((25OH) D) and intact parathyroid hormone (PTH) was done using chemiluminescence immunoassay using kits. Results: Out of 240, 115 were boys and 125 were girls. Out of 115 boys, vitamin D deficiency was seen in 20 (17.3%) and out of 125 girls in 26 (20.8%). Skin pigmentation score 1 was seen in 29, 2 in 10, 3 in 4 and 4 in 3. 30 were taken outdoor and 31were not using sunscreen. Season of visit among children with vitamin D deficiency was spring in 8, summer in 26 and autumn in 12. The difference was significant (P< 0.05). Conclusion: Authors found that vitamin D deficiency is a common health problem among children living in Ladakh and the frequency of vitamin D insufficiency was higher in girls than in boys.