Purpose <p>Human papillomavirus (HPV), the most common sexually transmitted infection, has been proposed as a potential factor in male infertility. This study aimed to assess the prevalence of HPV in semen samples from men undergoing in vitro fertilization (IVF) in Sweden and evaluate its association with semen parameters and embryological outcomes.</p> Methods <p>This prospective cohort study was conducted at Sahlgrenska University Hospital, Gothenburg, Sweden, between January 2023 and February 2024. Men (<i>n</i> = 246) undergoing IVF provided fresh semen samples for HPV DNA testing using real-time PCR. Semen analysis followed WHO guidelines, and fertilization and embryo quality assessments were conducted according to the Istanbul Consensus. Machine learning (ML) models were employed to predict fertilization and blastocyst formation outcomes.</p> Results <p>HPV was detected in 8.9% of semen samples. No significant differences in semen parameters were found between HPV-positive and HPV-negative men. However, in the non-male infertility subgroup, HPV-positive men had significantly higher total motility (median 65 vs. 60%, <i>p</i> = 0.021) and progressive motility (median 65 vs. 55%, <i>p</i> = 0.016). Similarly, in the unexplained infertility subgroup, progressive motility was higher in HPV-positive men (median 60 vs. 50%, <i>p</i> = 0.033). No significant differences were found in fertilization or blastocyst formation rates, and ML analysis confirmed that HPV presence did not influence predictive model accuracy.</p> Conclusion <p>HPV is detectable in the semen of a notable number of men undergoing IVF, but its presence does not significantly impact fertilization or embryo development. These findings suggest that routine HPV screening in semen may not be necessary for predicting IVF outcomes.</p> Trial registration <p>The study was registered on ClinicalTrials.gov (ID: NCT06161727).</p>