BACKGROUND External genital warts are a common sexually transmitted viral disease. We describe the patterns of treatment for initial presentations of external genital warts (EGWs) in Australian sexual health centers. METHODS This was a retrospective audit of 489 case notes from consecutive individuals who presented with a new diagnosis of EGWs to 1 of 5 major sexual health clinics in Australia. Eligibility criteria were consecutive patients aged 18 to 45 years inclusively, presenting with first ever episode of EGWs from January 1, 2004. Exclusion criteria were patients who were immunocompromised, including HIV infection, or enrollment in a treatment study for EGWs. RESULTS The median age at presentation of women was 23.2 years and of men 26.8 years. One quarter (n = 127) of patients had another sexually transmitted infection diagnosed at presentation. Nearly half of the patients (n = 224) presented only once for treatment. Most often, patients were treated with a monotherapy (n = 382/489; 78%), usually cryotherapy (257; 53%). Staff applied treatment in 361 (74%) cases. There was wide variation across sites, possibly reflecting local policies and budgets. We found no difference in wart resolution (n = 292; 60%) by initial treatment chosen. CONCLUSIONS The diagnosis and treatment of genital warts constitute a sizable proportion of clinical visits to the audited sexual health services and require a large input of staff time to manage, including the application of topical treatments. Our results help complete the picture of the burden of EGWs on Australian sexual health centers before the introduction of the HPV vaccine.