Merkel cell carcinomas are rare cutaneous neoplasms that are known to metastasize to various mucosal sites, including the genitourinary tract. Primary Merkel cell carcinomas of the genitourinary tract are extremely rare and may be mistaken for other more common carcinomas of the genitourinary tract, including urothelial carcinomas and prostatic carcinomas. However, primary Merkel cell carcinoma of the genitourinary tract is a very aggressive tumor with poor prognosis. Accurate diagnosis is crucial for appropriate clinical treatment. The discovery of the Merkel cell polyomavirus as a possible causative agent adds a new dimension in the understanding of the pathogenesis and diagnosis, and possible targeted therapies for this tumor.