The human bocavirus (HBoV), belonging to the genus of parvoviruses and pathogen of acute respiratory infection is known to persist latently in the infected host cells. There is increasing evidence that the virus plays an important role in cancerogenesis. The viral DNA has been detected in colorectal and lung tumors. Furthermore, pro-fibrotic and pro- cancerogenic cytokines were expressed in an HBoV infected cell culture system. Additionally unpublished whole transcriptome analysis show that several pathways leading to neoplasia are significantly upregulated after cell culture infection; for example, the matrix-metallo-proteinase 9 is substantially increased in head-and-neck cancers. In the present study we focused on the incidence of human bocavirus in tonsil squamous cell carcinomas compared to the occurrence of human papilloma virus. Therefore, formalin-fixed, paraffin-embedded tonsil tumor samples were screened for HBoV DNA and HPV DNA by PCR. The positive tissue sections were afterwards subjected to fluorescence in situ hybridization analysis. This technique enables us to identify HBoV and HPV DNA specifically in the host cells and to distinguish coinfection from single infection. In total 62 of 103 (60,2%) of the tonsil squamous cell carcinomas were tested positive for HBoV DNA and in 66 of 103 (64,1%) samples could be identified HPV DNA. The FISH analysis revealed that in case of coinfection with HBoV and HPV in 60% the virus DNA persisted in the same cells. This fact inspires the hypothesis that human bocavirus may contribute synergistically as a cofactor to tumor development in tonsils.