Introduction: Cutaneous warts are caused by human papillomavirus (HPV). Contrary to the painful ablative therapies associated with scarring and recurrence, immunotherapy (cell -mediated, anti-HPV response) adds to the therapeutic armamentarium. Objective: To compare therapeutic efficacy and safety of intralesional vitamin D 3 versus intralesional measles, mumps and rubella (MMR) vaccine in multiple cutaneous warts. Material and methods: This prospective, interventional, clinical comparative study was carried out on 96 patients with multiple cutaneous warts. The patients were enrolled after applying inclusion and exclusion criteria and were randomly divided into two groups of 48 patients each. Intralesional vitamin D 3 (group A) and intralesional MMR vaccine (group B) were administered at a maximum of 5 warts per patient for 4 sessions at fortnightly intervals with a follow-up visit at 3 months. The efficacy and safety of vitamin D 3 were compared to MMR vaccine using statistical tests. Results: A complete clearance of warts (injected and distant) was seen in 58.3% of cases (group A) and 52.1% of cases (group B), with no statistically significant difference. Filiform warts showed a better and faster response with vitamin D 3 compared to MMR vaccine. Both modalities were safe, with no major adverse effects except for a case of post-MMR vaccine orchitis. Conclusions: Immunotherapy with intralesional vitamin D 3 is as effective and safe as intralesional MMR vaccine in the treatment of cutaneous warts, with gratifying results in both local and distant warts.