The purpose of this study was to investigate the effects of low bone mineral density (BMD) risk factors and vitamin D receptor (VDR) and estrogen receptor alpha (ERα) gene polymorphisms on annual changes in BMD in collegiate female athletes. Participants were 239 female athletes belonging to a physical education university and were monitored about menstruation and injury for one year. A total of 173 participants (72.4%) were included in the statistical analysis because they completed all data. Total body, lumbar spine, and femoral neck BMD was measured by dual-energy X-ray absorptiometry at start of the experiment and one year later. VDR gene ApaI (rs7975232), TaqI (rs731236), and FokI (rs2228570) and ERα gene PvuII (rs2234693) and XbaI (rs9340799) polymorphisms were analyzed by TaqMan probe method. Multiple regression analysis performed for independent variables as BMI, menstrual cycle, stress fracture, sports type, and gene polymorphism and dependent variables as annual changes in each BMD site. Multiple regression analysis revealed that menstrual cycle and sports type were robust independent variables for lumbar spine and femoral neck BMD, respectively (β=−0.161, P=0.034; β=−0.184, P=0.016, respectively).These indicated that participants with amenorrhea were significant reduced lumbar spine BMD (−1.9%), and participation in endurance, aquatic, and esthetic type sports were significant reduced femoral neck BMD (−1.8%). In contrast, there were no significant differences in annual changes in BMD between any gene polymorphism and there were no interactions between low BMD risk factors and any gene polymorphisms. It suggests that annual changes in BMD in college female athletes may be reduced by amenorrhea and participating in endurance, aquatic and esthetic type sports, and may be unaffected by VDR gene ApaI, TaqI, and FokI and also ERα gene PvuII and XbaI polymorphisms in collegiate female athletes.