Objective: The role of Merkel cell polyomavirus (MCPyV) as a respiratory pathogen is controversial. The aim of this study was to determine the prevalence of MCPyV in patients with acute respiratory diseases and chronic lung diseases, including lung cancer, in order to evaluate the association between MCPyV infection and respiratory diseases. Methods: This study included 221 specimens (133 nasopharyngeal swabs and 88 lung biopsy specimens) obtained from patients with acute respiratory diseases and chronic lung diseases, including lung cancer. The detection of MCPyV was performed via nested polymerase chain reaction. Results: MCPyV positivity was 4.3% on average. All nasopharyngeal specimens were obtained from patients with acute respiratory diseases, and 8.2% of them were MCPyV DNA positive. There were no statistically significant differences in MCPyV prevalence according to age or gender. All specimens from nonmalignant chronic lung diseases and lung cancer were MCPyV negative. Conclusions: MCPyV was observed in specimens from patients with acute respiratory diseases, indicating that there may be a relationship between the virus and these diseases. We were not able to detect MCPyV in samples from patients with chronic lung diseases, including lung cancer, suggesting no association with MCPyV infection and no involvement of this polyomavirus in lung cancerogenesis.