Background- Persistent and recurrent warts pose a challenge to physicians. Despite the availability of multiple treatment options, warts are resistant to treatment. Intralesional Vitamin D3 and Autoinoculation both are promising treatment modality for multiple warts. AIM- To compare the efficacy and safety of intralesional Vitamin-D3 and autoinoculation in treating multiple warts. Patients and method- the study included 60 patients divided in two groups (group-A and group-B), each containing 30 patients. Informed consent was taken from each patient. Group-A patients received intralesional Vitamin-D3 0.2-0.5 ml every 3 weeks for maximum of four sessions. Group-B patients were treated by autoinoculation every 4 week for 3 sessions. RESULTS- At the end of 3 months 86.6% of patients showed response in group-A, Complete clearance was seen in 76.6% patients. Three months post autoinoculation (group-B), 66.6% patients showed response. Complete clearance was seen in 56.6% post autoinoculation in group-B. CONCLUSION- Intralesional Vitamin-D3 had the edge over Autoinoculation in palmoplantar, verruca vulgaris and periungual warts, while autoinoculation had the advantage in the plane variants.