Background: Viral warts are common infectious skin disease induced by human papillomavirus (HPV). But treatment of recalcitrant warts is still challenging. Objectives: In this study, we compared the effectiveness of Pulsed dye laser (PDL) and Long pulsed ND:YAG (LPNY) laser in the treatment of recalcitrant viral warts. Methods: We retrospectively analyzed the medical records of patients with recalcitrant warts treated with laser therapy between January, 2013 and February, 2016. Results: 72 patients with recalcitrant warts were evaluated. 39 patients were treated with pulsed dye laser and 33 patients were treated with LPNY laser. The following parameters were used: PDL (spot size, 7mm; pulse duration, 1.5ms; and fluence, 10-14 J/cm2), and LPNY (spot size, 5mm; pulse duration, 20ms; and fluence, 240-300 J/cm2). Complete clearance of 2 patients (5.1%) in PDL group, and 3 patients (9.1%) in LPNY group were observed without significant side effects. The patients who achieved at least 50% improvement from baseline were 20 (51.3%) in PDL, and 22 (66.7%) in LPNY, respectively. Conclusion: This research is meaningful because we compared the effectiveness of the PDL and LPNY in the recalcitrant warts. Both PDL and LPNY laser could be used as a safe and alternative treatment for recalcitrant warts.