The JC virus is a widely infected human polyomavirus. Recent foreign researches showed that the JC virus infection is correlated with tumors of nervous system and digestive system, while, and study on the relationship between JC virus infection and gynecological tumor is seldom reported. In this study, we first establish the nucleic acid detection methods and procedures for JC virus and its highly homologous BK virus. The JC and BK viruses infection was evaluated by detect the viral DNA in samples including biopsy tissues, serum as well as urine of myoma of uterus (98 cases), cervical cancer (84 cases), endometrial cancer (40 cases) and ovarian tumor (72 cases) patients. The BK viral DNA positive rate was significantly higher in urine samples than that of blood and biopsy samples, and there is no significant difference of the BK viral DNA positive rate among all patient groups. The JC viral DNA positive rate is almost 0 in serum samples and biopsy. tissues, however, viral DNA positive rate is more than 50% in urine samples. In fibroids group, the JC viral DNA positive rate is up to 65. 3% which is significantly higher than that in other patients groups and healthy control. Further gynecological tumor associated viruses detection showed that only human papilloma virus infection is associated with cervical cancer, the herpes simplex virus, EB virus and cytomegalovirus infection is extremely low in our patient groups. No synergistic effect on gynecological tumor caused by viruses co-infection was observed. Our study showed that JC virus infection is highly related to the pathogenesis of uterine fibroids.