Background Many therapeutic modalities are available for treating genital warts; however, the effectiveness of both diphenylcyclopropenone and podophyllin is still controversial. Aim To evaluate the effectiveness and safety of diphenylcyclopropenone and podophyllin in treating genital warts. Methods This study included 57 patients, divided randomly into two groups. Group (A): diphenylcyclopropenone ( n = 29). Group (B): podophyllin 25% ( n = 28). In group (A), sensitization was done with 2% diphenylcyclopropenone. Then, after 1 or 2 weeks, treatment started with a weekly application of diphenylcyclopropenone solutions ranging between 0.001 and 1% until clearance, or for a maximum of 10 sessions. In group (B), podophyllin 25% was applied weekly until clearance or for a maximum of 6 weeks. Results Higher clearance was achieved in group A, with 19 of 29 (65.5%) patients, than in group B, with 9 of 28 (32.1%) ( p-value = 0.004). Also, effectiveness increases with young age in group A. Shorter wart duration was associated with better response in both groups ( p-value = 0.005). No serious adverse effects occurred in either group. No recurrence was detected in group A, while seven patients (77.8%) had recurrence in group B after 1 year of follow up. Conclusion Diphenylcyclopropenone shows a higher success rate than podophyllin in treating genital warts and a lower recurrence rate.