Human papillomavirus (HPV) is the most common sexually transmitted viral infection worldwide, which has been suggested to affect male fertility. However, reported evidence is scarce and inconclusive. Moreover, the putative effects of coinfections remain unveiled. In the present study, we analyzed male urogenital infection by HPV and coinfection with several other uropathogens, sperm quality and biomarkers of semen inflammation in a cohort of 205 men attending a urology clinic. A considerable prevalence (19%) of HPV male urogenital infection was found. Interestingly, HPV was detected coinfecting with at least one other uropathogen in most cases (74.4%). Notably, the most frequently detected coinfection was C. trachomatis (CT, 52% of cases). Remarkably, patients solely infected with HPV showed no significant alterations in conventional sperm parameters as well as reduced concentrations of IL-6 and leukocytes in semen. However, patients coinfected with HPV and CT showed significantly impaired sperm concentration and motility and increased levels of IL-6 in semen. These results indicate that HPV infection alone does not significantly alter sperm quality. However, the coinfection with CT decreases sperm quality and induces semen inflammation, suggesting that concurrent HPV and CT infection in semen represents a distinct clinical entity with particular characteristics.