Viral infections including latent viruses have been known to affect semen quality of men negatively thereby affecting reproductive potentials. A cross-sectional study was done to assess the prevalence of CMV antigen/ antibody (IgG and IgM), HBV, HCV, HIV, confirm CMV molecularly and determine their risk factors for infection. Blood and semen samples were collected from 96 apparently healthy men aged between 24 – 65years in Onitsha, South-East, Nigeria. Ethical approval and informed consents were obtained. Data was collected using structured questionnaires and standard WHO tool for STDs. Method: HBV and HCV antibodies were screened immunochromatographically; HIV tested by parallel method, confirmed using Western-blot; CMV IgG and IgM were screened using ELISA, confirmed molecularly with quantitative PCR. Data was assessed using SPSS version 23 set at 0.05 at 95% confidence interval. Result: This revealed that CMV IgG had the highest prevalence of 68(70.8%) (p=0.04), HIV had 2(2.1%) (p=0.904) and HCV had 1(1.0%) (p=0.167). None of the subjects tested positive to CMV IgM and HBV. One out of 17 samples tested positive for CMV qPCR 1(5.9%). HIV was significantly associated with multiple partners (p=0.002) and unprotected anal sex (p=0.019). Conclusion: Early screening and treatment should be done for a more quality health and reproductive life.