Male genital tract infections have been associated with infertility, and Escherichia coli has drawn increasing attention as an important bacterium in this context. This investigation aimed to characterize and compare the distributions of O-antigen serogroups of E. coli in the semen samples of fertile and infertile men. Methods: In this case-control study, semen samples were collected from 618 fertile and 1,535 infertile men. The E. coli-positive samples were evaluated in terms of concentration, morphology, viability, and motility parameters according to the World Health Organization 2010 guidelines. Finally, different serogroups of E. coli were identified by multiplex polymerase chain reaction targeting the O-antigen variations of the bacterium. Results: The prevalence of E. coli among fertile men was significantly higher than among infertile men (p<0.001). The sperm morphology, viability, and motility in the E. coli-positive fertile group were significantly higher than in the E. coli-positive infertile group (p<0.001). E. coli O6 was the most prevalent serogroup found in both groups. However, there was no significant difference in the frequency of different serogroups of E. coil between the two groups (p=0.55). Conclusion: Despite the higher prevalence of E. coli among fertile men, E. coli had more detrimental effects on semen parameters in infertile men. There was no significant difference in E. coli serogroups between the fertile and infertile groups.