Abstract Background: Human Polyomaviruses such as MCPyV and HPyV6 are frequently found as part of healthy skin microbiota and have been associated with Merkel cell carcinoma (MCC), pruritic and dyskeratotic dermatoses, respectively. Their presence in other types of skin conditions varies greatly depending on lesion type and population. Objectives: To analyse comparatively the presence of MCPyV and HPyV6 in nonmelanoma skin cancers and healthy skin. Methods: The authors utilized qPCR techniques to quantify these pathogens in NMSC, premalignant diseases, and healthy skin of 87 patients. Results: MCPyV was detected in over 40% of samples, while HPyV6 was in 9.6%. MCPyV load was higher in squamous cell carcinomas (SCC) compared to basal cell carcinomas (BCC) (p = 0.016) and HPyV6 showed a higher percentage of infected cells in areas of low solar exposure as well as normal skin (p = 0.012). A fair agreement (kappa = 0.301) was found between MCPyV detection in lesions and their respective perilesional skin, indicating a random process of local dissemination of the virus. Study limitations: The lack of a larger sampling of different lesion types and protein expression analyses limits the correlation findings. Conclusions: This is the first report of HPyV6 detection in the healthy skin of a Brazilian population, but the role of both polyomaviruses in NMSC has yet to be demonstrated.