The increasing incidence of genital warts has led to more public awareness of this infection and its possible sequelae. Currently available treatment remains unsatisfactory, and there is pressure to develop effective and convenient alternatives. Podophyllotoxin is standardised and stable, whereas podophyllin has a variable composition. In an open comparison of self applied podophyllotoxin 0.5% versus podophyllin 20% applied by a doctor to treat external penile warts, podophyllotoxin was more effective and gave quicker resolution than podophyllin. Side effects were similar for both preparations, and few patients experienced complications severe enough to stop treatment. Podophyllotoxin can therefore be used safely and effectively for home treatment monitored at an outpatient clinic and provides a useful alternative to treatment with podophyllin at overburdened genitourinary medicine clinics.