The aim of the present study was to determine the distribution of high-risk human papillomavirus (HR-HPV) genotypes in childbearing age women, teenage girls, HIV-infected women, women with high-grade precancerous lesions and cervical cancer, sex workers, men, and otolaryngology tumor cases in Burkina Faso. This descriptive cross-sectional study with several target groups, consisted of 2386 samples from Burkina Faso. HR-HPV genotypes were characterized using real-time multiplex PCR. The prevalence of HR-HPV ranged from 15.63 to 72.31% depending on the target population and the nature of the samples. The most predominant genotypes in descending order were HPV-56, HPV-52, HPV-39, HPV-59, HPV-51, HPV-35, HPV-31, HPV-18, HPV-68, HPV-16, HPV-66, HPV-58, HPV-45, and HPV-33. The results of the present study show a wide variation in the distribution of HR-HPV genotypes in Burkina Faso. Genotypes 16 and 18 covered by HPV vaccines only accounted for 32.23% of HR-HPV cases.