Background: The prevalence of anogenital warts is increasing in adults as well as in pediatric population. The treatment of anogenital warts is challenging, particularly in children as most conventional modalities are painful and associated with high recurrence rates. Objectives: To evaluate the efficacy and safety of intralesional immunotherapy for the treatment of anogenital warts in pediatric patients. Methods: Forty child presenting with multiple anogenital warts were randomly assigned into 3 groups. The first group (15 patients) received intralesional MMR vaccine, the second group (15 patients) received intralesional Candida antigen and the third group (10 patients) received intralesional saline as a control. Each modality was injected into the largest wart at 2-week intervals until complete clearance or for a maximum of 5 sessions. Results: Highly significant difference was found between the therapeutic response of anogenital warts to both MMR vaccine and Candida antigen compared to intralesional saline (p = .005). No significant difference was observed between MMR vaccine and Candida antigen groups (p = .885). Side effects were mild and no recurrence was detected in the 6 month follow-up period. Conclusions: Intralesional immunotherapy is a promising effective and well-tolerated treatment modality for multiple anogenital warts in children.