Warts are common problems affecting adults and children. Multiple treatment options are available, but no single therapy stands out as uniformly effective. Propolis and Echinacea are relatively safe immunomodulators with antiviral properties. The purpose of this study was to assess the efficacy of Propolis and Echinacea in treating different types of warts. In a single-blind, randomized, 3-months trial, 135 patients with different types of warts received oral Propolis, Echinacea, or placebo. In patients with plane and common warts treated with Propolis, cure was achieved in 75% and 73% of patients, respectively. These results were significantly better than those associated with Echinacea treatment or placebo. We conclude that Propolis is an effective and safe immunomodulating therapy for plane and common warts.