Adeno-associated virus (AAV) and human papillomavirus (HPV) DNAs were found in abnormal quality semen, early abortus and female genital tissues. It was suggested that they might cause male infertility and miscarriages. This study was performed to determine the detection rate of these viruses in the semen and to assess the relationship between the presence of virus and male factor infertility and recurrent miscarriages. Sixty-three of 99 recruited male were included in this study according to the completeness of follow-up and the sample availability. Fourteen male with normal reproductive capacity were allocated to control group, 15 male with abnormal results in semen analysis were grouped as male factor infertility (MF) group, and 34 male whose spouses have had history of repeated spontaneous abortions were designated as repeated miscarriage (RM) group. AAV and HPV were detected in semen by polymerase chain reaction. The detection rate of AAV in the MF infertility group and RM group was 60.0% and 50.0%, respectively, while 14.3% in the control group (p < 0.05). However, the differences in the detection rate of HPV were not statistically significant among groups. These results suggest that AAV could be related to repeated miscarriages and male infertility.