Intralesional (IL) vitamin D3 is an emerging treatment for cutaneous warts. However, its effectiveness and exact mechanism is not fully evaluated. We aimed to compare the efficacy and safety of IL purified protein derivative (PPD) and IL vitamin D3 in multiple warts and to investigate their systemic effect clinically and immunologically. Forty-five patients with multiple extragenital warts were treated with IL-PPD (22 patients) or IL vitamin D3 injection (23 patients) for a maximum of three sessions at 3 week intervals. Decrease in size and number of warts and adverse effects were evaluated. Serum interleukin-12 (IL-12) and interferon-gamma (IFN-γ) levels were measured before and 3 weeks after the last session. Higher clearance rates for all warts were observed with IL-PPD compared to IL vitamin D (59.1% vs. 21.7% complete clearance, p < .001). Significant increase was found in both serum IL-12 and IFN-γ after PPD treatment (p = .034 and p = .04, respectively), but only IFN-γ after vitamin D3 treatment (p = 0.02). Both IL vitamin D3 and PPD showed positive results in treatment of multiple warts. However, PPD showed higher clinical efficacy and more increase in both IL-12 and IFN-γ levels.