Background: Intralesional immunotherapy has been effectively used in the treatment of warts; however, comparative studies between different antigens are limited. Objective: To evaluate the efficacy and safety of intralesional measles, mumps, and rubella (MMR) vaccine compared with intralesional Candida antigen for the treatment of multiple common and plantar warts. Methods: Sixty-eight adult patients with multiple common and plantar warts were randomly assigned into two groups, each containing 34 patients. The first group received intralesional MMR vaccine, while the second group received intralesional Candida antigen. Each treatment was injected into the largest wart at 2-week intervals until complete clearance or for a maximum of 5 sessions. Results: The overall therapeutic response was higher in the Candida antigen group (73.5%) compared with the MMR group (67.7%); however, the difference was not statistically significant. Complete clearance of common warts was higher in the Candida antigen group, while that of plantar warts was higher in the MMR group. Adverse effects were transient and well tolerated in both groups. No recurrence was detected during the 6-month follow-up period. Conclusion: Intralesional MMR and intralesional Candida antigen showed comparable efficacy and safety in the treatment of common and plantar warts.