Merkel cell carcinoma (MCC) is a rare neuroendocrine carcinoma typically affecting the elderly. Only 5% to 10% of the patients are younger than 50 years at the time of the diagnosis. The purpose of this study was to compare the tumour and disease characteristics between exceptionally young and the typical elderly MCC population. Further, quantitative polymerase chain reaction analysis was used to study for Merkel cell polyomavirus (MCPyV) in their primary MCC tumours. Patients diagnosed with MCC in Finland from 1979 to 2004 were identified from the files of the Finnish Cancer Registry. Presence of MCPyV DNA in tumour samples was investigated using quantitative polymerase chain reaction. Six of 181 MCC patients were ≤50 years, with male-to-female ratio of 1:1. An altered immune condition state was observed in five patients. The Kaplan–Meier analysis showed a trend towards worse MCC-specific survival both in 5- and 10-year surveillance for younger patients. Five primary tumour tissue samples, available for analysis, contained MCPyV DNA. Our data shows that MCC, ≤50 years of age, is rarer then previously estimated. Moreover, our data showed marked differences both in patient demographics and in primary tumour characteristics as compared to surveys including older MCC patients. Course of disease seemed to be worse in the exceptionally young patients. All MCC primary tumours in this study contained MCPyV DNA.