The association between air pollution and bone health was evaluated in adolescents in the city of Tehran. This study is essentially ecological. Vitamin D deficiency among adolescents has been reported at higher rates in polluted areas than in non-polluted areas. Additionally, residence in polluted areas is associated with lower levels of bone alkaline phosphatase. Purpose The aim of this study was to evaluate the association between ambient air pollution and bone turnover in adolescents and to compare the prevalence of vitamin D deficiency between polluted and non-polluted areas of Tehran. Methods This cross-sectional population-based study was conducted on 325 middle-and high-school students (both girls and boys) in Tehran in the winter. During the study period, detailed daily data on air pollution were obtained from archived data collected by Tehran Air Quality Control Company (AQCC). Serum levels of calcium, phosphorus, parathyroid hormone (PTH), bone-specific alkaline phosphatase, 25(OH) vitamin D, osteocalcin, cross-linked Ctelopeptide (CTX), total protein, albumin, and creatinine were obtained from the study group. Results Vitamin D deficiency was more prevalent in polluted areas than in non-polluted areas. After adjustment for age and sex, residence in the polluted area showed a statistically significant positive association with vitamin D deficiency and a statistically significant negative association with bone turnover. Interestingly, high calcium intake (>5000 mg/week) protects against the effects of air pollution on bone turnover. Conclusions Air pollution is a chief factor determining the amount of solar UVB that reaches the earth's surface. Thus, atmospheric pollution may play a significant independent role in the development of vitamin D deficiency.