Background: The role of exercise in osteoporosis prevention has been proven. Nevertheless, there is no consensus about the types of sports, especially at professional levels. Non-impact sports such as swimming may have a negative effect or no effect. Objectives: Thus, the present study aimed to compare the effect of different sports on bone mineral content (BMC) and bone mineral density (BMD) of elite female athletes. Methods: This was a cross-sectional study consisting of 48 athletes in five groups of long-distance running, volleyball, basketball, swimming (n = 12 for each), and ten control subjects. For measuring the lumbar spine (L2 - L4) and proximal femur (femoral neck, trochanter, and Ward’s triangle), the dual-energy X-ray absorptiometry (DEXA) method was applied. Results: Indicated that the running, basketball, and volleyball groups had a significantly higher lumbar spine and proximal femur BMD than the swimming and control groups (P < 0.05). Running resulted in significantly higher lumbar spine BMC compared to volleyball, basketball, swimming, and control groups, respectively (P < 0.01), while basketball had higher proximal femur BMC than running and controls (P < 0.01). The Z-score of the lumbar spine in the running was significantly higher than in basketball, swimming, and controls (P < 0.05), while basketball had a significantly higher femur neck Z-score than volleyball, running, and controls (P < 0.001). Finally, the swimmers had significantly higher Z-scores in the lumbar and the proximal femur than non-athletes (P < 0.001). Conclusions: Although all sports are effective for improving the bone health, the swimmers had much better bone status than non-athletes, while the sports of long-distance running and basketball were more efficient than others; therefore, a combination of endurance and jumping exercises seems to be the best way to prevent osteoporosis.