Background Human papillomavirus (HPV) infection is a public health problem in Africa because of its frequency and its various consequences in both men and women. In Burkina Faso, there is little data on the carriage of HPV infection in male subjects. This study aimed to determine the carriage of HPV infection in male subjects in Ouagadougou, Burkina Faso.Methods This was a cross-sectional study conducted from December 2015 to September 2016. During this study period, a total of 124 male subjects who gave informed consent were recruited as part of a fertility assessment. Semen samples were analyzed by Real- Time PCR using Real TM Quant High Risk Screen HPV kit to detect 14 high-risk HPV genotypes. The Chi square test was used for comparisons.Results Of the 124 male subjects, 22 were positive for at least one high-risk HPV, with a prevalence of 17.7%. HPV 56 was the most represented genotype with a frequency of 20%, followed by HPV 39 (11%) and HPV 68 (11%), HPV 16 (8%). The genotypes HPV 18, HPV33, HPV35, HPV51 and HPV52 also had the same frequency of 6% each and the HPV 31, 45, 59 and 66 had the same frequency of 3% each. Of the 22 positive cases, 10 were multiple infections. Spermocytogram of patients showed at least one abnormality in 87.9% of cases. Necrozoospermia and oligozoospermia were the most abnormalities observed with 42% and 40% respectively followed by asthenospermia (18%); teratozoospermia (16%) and azoospermia (14%).Conclusion This study showed that like women, men are infected by HPV with a relatively high prevalence. In addition, the predominant genotypes in the male subjects of this study are not those targeted by the HPV vaccines available in our countries. Hence the need to reinforce the strategies for controlling HPV infection and HPV prophylactic vaccination for young boys.