The verrucous cyst is a non-plantar epidermoid cyst with histopathological features of human papillomavirus (HPV) infection, including papillomatosis and hypergranulosis of the cyst lining. We report the first case of a verrucous cyst demonstrating not only the histopathological and immunohistochemical features of HPV infection, but also homology with HPV type 59 on HPV genotyping. A 28-year-old male developed a palpable mass in his right flank. Histological examination revealed an intradermal cyst lined by an acanthotic and papillomatous squamous epithelium with prominent keratohyaline granules and squamous eddies. The keratinocyte nuclei were positive for papillomavirus antigens on immunohistochemistry and HPV genotyping demonstrated a homology to HPV type 59, a high-risk genital type. Although we only experienced a single case with such a finding, we suggest that it may be necessary to subject patients with verrucous cysts to a closer follow up for better characterization of their clinical behavior.