Objective Having vitamin D levels within normal limits is important for bone and muscle health and its deficiency may increase the risk of injury. The aim of this cross-sectional study was to investigate whether vitamin D levels are different in indoor and outdoor athletes and its levels increase the risk of injury. Material and Methods Serum vitamin D levels were measured in Caucasian adolescent athletes, who admitted to the sports medicine polyclinic due to a routine health check or injury. The study was carried out at 38 degrees 26 ' north latitude in Izmir between June and September 2019. After the physical examination of the injured athletes, the diagnoses were made accompanied by the findings obtained by imaging methods in cases of necessity. Results A total of 256 athletes, including swimmers (n = 87), basketball players (n = 104), and football (n = 65) players aged 13.2 (+/- 2.2) years, were investigated. The average serum vitamin D (25(OH)D) level in athletes was 29.2 (+/- 10.0) ng/mL (6.0-66.0 ng/mL). Forty-six of all athletes (18%) had vitamin D deficiency, with a mean value of 15.7 (+/- 4.0) ng/mL, and 93 of them (36.3%) had vitamin D deficiency with a mean value of 25.2 (+/- 2.4) ng/mL. While vitamin D levels were significantly higher in football players (32 ng/mL) than in other athletes (p < 0.05), it was similar in basketball players (27 ng/mL) and swimmers (26 ng/mL) (p > 0.05). Vitamin D levels (26 ng/mL) of the injured athletes were significantly lower than those of the non-injured athletes (30 ng/mL) (p = 0.001). Bone injuries were significantly related to Vitamin D levels (p < 0.001) but not with muscle injuries (p > 0.05). Conclusion Frequency of vitamin D deficiency and insufficiency is higher in indoor athletes andis especially associated with risk of bone injuries . In order to examine the effect of vitamin D level on bone mineral density, comprehensive prospective studies are required.