The objective of the study was to determine the cost implications of patterns of treatment for patients with external genital warts. A retrospective case note review was carried out at six genitourinary medicine (GUM) clinics in the UK. Significant variations in the total costs of care were observed across the clinics and across the choice of therapy. The cost per successful outcome was ?221.81 for males and ?211.07 for females. A minority of patients accounted for the majority of costs, for example the 30.1% of male patients who recorded six or more visits contributed 66.2% of the total cost. Costs also varied significantly by therapy sequence chosen. Patients who remained on their initial therapy experienced the lowest costs, with the extent to which patients shifted therapies substantially impacting on costs. Therapy sequences involving podophyllin were found to be the most expensive options in achieving a completed episode of care. We concluded that a high proportion of costs for GUM clinics is due to the failure of the initial therapy and by subsequent therapy switching. A greater emphasis on the selection of alternative treatment options, such as the patient-applied therapies, may help to reduce overall costs of care.