A clear etiopathogenetic concept for atypical fibroxanthoma (AFX) is not established yet. Nevertheless, AFX is known as a pleomorphic but indolent tumor primarily of the elderly and/or immunosuppressed patient occurring in severely sun- or radiation-damaged skin. These risk factors are almost identical to those of Merkel cell carcinoma (MCC), a highly malignant skin tumor being thought to be pathogenetically associated with the recently discovered Merkel cell polyomavirus (MCPyV). Because AFX and MCC share risk factors, the aim of this study was to evaluate presence of MCPyV DNA in 23 cases of AFX by PCR and direct DNA sequencing. Subsequently, we correlated clinical features with MCPyV DNA status in AFX. We detected MCPyV DNA in 4 of 23 AFX. All patients with MCPyV DNA-positive tumors were men. The mean age of patients with MCPyV DNA-positive AFX was 84.8 ± 8.7 years (vs. 75.2 ± 7.8 years of MCPyV DNA-negative AFX), the mean duration of tumor growth was 4.5 ± 2.3 months (vs. 5.1 ± 2.8 months) and the mean tumor diameter was 1.2 ± 0.3 cm (vs. 1.3 ± 0.7 cm). Ulceration was present in 75% of MCPyV DNA-positive tumors (vs. 65.2%). In conclusion, MCPyV DNA is present in 17% of AFX, in this cohort affecting predominantly male patients with higher age (>80 years). Clinical features seem to be independent of MCPyV DNA status. Although the role of MCPyV is unclear in this setting, it may act as a cofactor in the tumorigenesis of AFX in a subset of cases.