The incidence of tonsillar carcinomas associated with Human Papillomavirus (HPV) infection has increased dramatically over the last three decades. In fact, currently in Scandinavia, HPV-associated cases account for over 80 % of tonsillar carcinoma cases. Yet, the epidemiology and natural history of tonsillar HPV infections remains poorly characterized. Our aim was to characterize such infections in the Danish population in tumor-free tonsillar tissue. Unlike previous studies, we considered both palatine tonsils. We examined both tonsils from 80 patients with peritonsillar abscess (n = 25) or chronic tonsillar disease (n = 55). HPV was detected by nested PCR with PGMY 09/11 and GP5+/GP6+L1 consensus primers, and typed by sequencing. Samples were also analyzed using a higher-throughput method, the CLART HPV 2 Clinical Array Assay. The overall prevalence of HPV tonsillar infection was 1.25 % (1/80, 95 % CI 0.03-6.77 %) by nested PCR, and 0 % by CLART HPV2 Clinical Array. The HPV-positive patient was a 16-year-old female with recurrent tonsillitis and tonsillar hypertrophy. The type detected was HPV6. HPV was not detected in the contralateral tonsil of this patient. Compared to cervical HPV infections in Denmark, tonsillar HPV infections are 10- to 15-fold less frequent. In the HPV-positive patient in this study, HPV was detected in only one of the tonsils. This raises the possibility that prior studies may underestimate the prevalence of HPV infections, as they do not consider both palatine tonsils.