Common benign masses in the subungual space include glomus tumor, subungual exostosis, keratoacanthoma, epidermal cyst and mucoid cyst. These are usually accompanied by pain and cause onychodystrophy. Malignant tumors such as squamous cell carcinoma and malignant melanoma also could occur in subungual space. A 16-year-old female presented to our department with a 2-year history of asymptomatic subungual flat plaque on the second finger. Physical examination revealed a well-demarcated 0.5 x 0.7-cm-sized, irregularly shaped, skin-colored to yellowish flat plaque on the left second finger with onycholysis. She was treated with a topical gel mixture of bethamethasone and calcipotriol and an intra-lesional steroid injection under the initial impression of onychodystrophy. After 5 months of treatment, the lesion showed no progress, so nail bed punch biopsy was performed after partial nail plate removal. Histopathological examination revealed a mild papillomatosis, many koilocytotic atypia of the epidermis, and dilated capillary vessels in the upper dermis, consistent with a viral wart. Human papilloma virus genotyping by real-time PCR confirmed HPV type 53 infection. Herein, we report a rare case of subungual wart caused by HPV type 53.