Merkel cell carcinoma (MCC) is a rare cutaneous neuroendocrine carcinoma. The aims of this study were to investigate the expression of the transcription factors B-lymphoma Moloney murine leukaemia virus insertion (BMI1), myelocytomatosis viral oncogene homologue (c-Myc) and Snail in MCC tumour specimens and to examine the relationship of these markers to Merkel cell polyoma virus (MCV). The study comprised of 133 patients with primary MCC. The expression of BMI1, Snail and c-Myc protein was assessed by immunohistochemistry and compared with clinical parameters, MCV status and patient survival. The presence of MCV was inversely correlated with the expression of BMI1 protein. Tumours expressing BMI1 protein more often presented with lymph node metastases. Snail protein expression was decreased in cases with metastatic dissemination. This study identified two subgroups of MCC: tumours expressing BMI1 but negative for MCV DNA and tumours negative for BMI1 expression but positive for MCV. Importantly, BMI1-positive cases often presented with lymph node metastases. Combined, these results suggest that subtypes of this malignancy exist.