Although there are many reports about the risk of breast cancer, few have reported clinical factors including history of breast-related or other diseases that affect the prevalence of breast cancer. This study explores these risk factors for breast cancer cases reported in Beijing in 2009.Data were derived from a Beijing breast cancer screening performed in 2009, of 568,000 women, from 16 districts of Beijing, all aged between 40 and 60 years. In this study, multilevel statistical modeling was used to identify clinical factors that affect the prevalence of breast cancer and to provide more reliable evidence for clinical diagnostics by using screening data.Those women who had organ transplants, compared with those with none, were associated with breast cancer with an odds ratio (OR) = 65.352 [95% confidence interval (CI): 8.488-503.165] and those with solid breast mass compared with none had OR = 1.384 (95% CI: 1.022- 1.873). Malignant tendency was strongly associated with increased risk of breast cancer, OR = 207.999(95% CI: 151.950-284.721). The risk of breast cancer increased with age, OR1 = 2.759 (95% CI: 1.837-4.144, 56-60 vs. 40-45), OR2 = 2.047 (95% CI: 1.394-3.077, 51-55 vs. 40-45), OR3 = 1.668 (95% CI: 1.145-2.431). Normal results of B ultrasonic examination show a lower risk among participants, OR= 0.136 (95% CI: 0.085-0.218). Those women with ductal papilloma compared with none were associated with breast cancer, OR=6.524 (95% CI: 1.871-22.746). Therefore, this study suggests that clinical doctors should pay attention to these high-risk factors.