Merkel cell polyomavirus (MCPyV) is associated with Merkel cell carcinoma (MCC), a rare skin malignancy. Human polyomavirus six and seven (HPyV6 and HPyV7) were identified on a skin but have not been associated with any pathology. The serology data suggest that infection with polyomaviruses occurs in childhood and they are widespread in population. However, the site of persistent infection has not been identified. Altogether, 103 formalin‐fixed paraffin‐embedded (FFPE) specimens and five fresh frozen tissues (FF) of non‐malignant tonsils and 97 FFPE and 15 FF samples of tonsillar carcinomas were analyzed by qPCR for the presence of MCPyV, HPyV6, and HPyV7 DNA. All MCPyV DNA positive FF tissues were screened for the expression of early viral transcripts. Overall prevalence of MCPyV, HPyV6, and HPyV7 in non‐malignant tonsillar tissues was 10.2%, 4.6%, and, 0.9%, respectively. The prevalence of MCPyV DNA in non‐malignant tonsils increased with age (P < 0.05). While the prevalence of MCPyV DNA was significantly higher in the tumors than non‐malignant tissues (35.7% vs. 10.2%) (P < 0.001), the prevalence of HPyV6 DNA (5.4% vs. 4.6%) and HPyV7 DNA (1.8% vs. 0.9%) were comparable. In all MCPyV DNA positive FF tissues early transcripts were detected. MCPyV, HPyV6, and HPyV7 DNAs were found in tonsils, suggesting that the tonsils may be a site of viral latency. The viral load was low indicating that only a fraction of cells are infected. The higher prevalence of MCPyV DNA was detected in tonsillar tumors but there was no difference in the viral load between tumor and healthy tissues. J. Med. Virol. 88:695–702, 2016. © 2015 Wiley Periodicals, Inc.