Cutaneous warts are caused by human papillomavirus (HPV) infection. Distinguishing plantar warts from clavus and tylosis can be difficult. A less-invasive method of examining these lesions is necessary. Previously, we collected data on 90 patients with warts and related diseases to explore differentiation methods using HPV typing of tissue from the wart surface. In that study, 21 patients were diagnosed as cases with plantar warts, however, 10 of those 21 cases showed HPV-negative by polymerase chain reaction analysis, causing some ambiguity, thus their outcomes should be confirmed. To assess the role of HPV typing in clinical practice, we followed up these 21 cases (11 HPV-positive and 10 HPV-negative) and analyzed their outcomes. The HPV-positive group included HPV1a (one case), HPV27 (four cases), HPV57 (three cases), and HPV65 (three cases). The median age of the 21 patients was 43 years, that of the 11 HPV-positive cases was 37 years, and that of the 10 HPV-negative cases was 44 years. The sex ratios (male:female) of the HPV-positive and HPV-negative groups were 6:5 and 2:8, respectively. All 21 patients were treated with liquid nitrogen after surface keratin removal, concomitant with salicylic acid topical plaster or oral administration of Yokuinin. The longest follow-up period was 548 days. Kaplan-Meier analysis was performed to assess the healing rate according to HPV-positivity. The healing rate in HPV-positive cases was significantly higher than in HPV-negative cases (P = 0.001). Although the sample size was small, the results suggest HPV typing using non-invasive surface materials facilitates accurate diagnosis and prevents prolonged treatment of plantar warts.