Neisseria gonorrhoeae is a member of the Neisseriaceae family. They are non-spore-forming, gram-negative, encapsulated, non-motile, non-acidic, and bean-shaped bacteria. This study included 40 men that presented chronic and recurrent infection with N. gonorrhoeae virus. The initial infection of this virus was detected using a rapid bacterial antigen immunoassay and confirmed using enzyme-linked immunosorbent assay (ELISA ). The mean age of the study group was 36.71±12 (mean±) years. Men between the age of 20-49 years were the most affected by N. gonorrhoeae infection, and displayed a significantly lower average sperm count than the healthy individuals upon semen examination. The percentage of sperms with slow motility, total number of dead sperms, and abnormal- shaped sperms were some significant phenotypes observed in the infected individuals as compared to that in the healthy controls. In this study, we found that the bacterium, N. gonorrhoeae could cause erosion of the mitochondrial DNA of sperms in the semen of the infected individuals. In addition, using the gap-PCR technique, it became evident that the infected individuals portraying altered sperm characteristics as mentioned above, showed increased number of common deletion (4, 977 base pairs) in the sperm mitochondrial (mt)-DNA. Hence, our results imply that N. gonorrhoeae infection can lead to a common deletion of 4,977 bp in sperm mt–DNA, which can in turn cause male sterility.