Acne vulgaris is an extremely common skin disorder that can be treated effectively with drugs that are currently available. Poor compliance, however, is a major factor in the high failure rates seen in acne treatment. Compliance might be enhanced by considering patient preferences for acne medications. Conjoint analysis is well suited for the study of patient preferences in healthcare, but is novel to the field of dermatology. The study aimed to determine and compare patient preferences for four topical antibiotics used for 1 week, once or twice daily, to treat acne vulgaris. A randomised, phase IV, single-centre, cross-over study was performed using conjoint analysis and a traditional patient questionnaire. Over 4 weeks, the patients used each of four topical antibiotics for 1 week: erythromycin/zinc solution, clindamycin phosphate lotion, benzoyl peroxide (BP)/erythromycin gel (each applied twice daily) and clindamycin phosphate gel (applied once daily). The conjoint analysis examined five different attributes of acne medications: form, storage, product life once opened, method of application and regimen (each with two or three possible options). From 108 possible permutations of the five attributes, 16 hypothetical medications were selected at random and described on printed cards. Pre- and post-treatment, the patients ranked the cards in order of preference and rated each hypothetical product based on their likelihood to use it. For each patient, product 'utilities' were then calculated by multiple regression. The patients also completed a patient acceptability questionnaire, by which they rated the product acceptability after 1 week of treatment with each of the four topical antibiotics. The patients later ranked the medications in order of preference after using all four treatments. Adverse events were recorded in diary cards to assess tolerability. Of 67 patients recruited, 64 used all four medications and completed the study. The conjoint analysis found that a gel formulation, room temperature storage, product life of up to 18 months once opened, application with fingers and once-daily regimen were the options ranked first for the five product attributes. According to the ranking order (out of 108) for the combination of attributes representing the four study medications, clindamycin phosphate gel had the highest rankings (6 and 1 pre- and post-treatment, respectively) and BP/erythromycin gel had the lowest rankings (93 and 70 pre- and post-treatment). The rankings of clindamycin phosphate lotion and erythromycin/zinc solution worsened from pre- to post-treatment, indicating a shift in patient preference after they experienced products 'in-use' during the study. Based on the questionnaire, clindamycin phosphate gel was liked best by the highest proportion of patients (33%). In terms of overall satisfaction, the order of preference was: (i) clindamycin phosphate gel, (ii) clindamycin phosphate lotion, (iii) BP/erythromycin gel and (iv) erythromycin/zinc solution. Adverse events related to medication occurred most frequently with erythromycin/zinc solution and BP/erythromycin gel. Clindamycin phosphate gel was the only product not associated with any episodes resulting in a change of medication or dose. Conjoint analysis provided a convenient, reliable tool for assessing patient preferences for topical antibiotics used to treat acne. The patients clearly preferred a gel formulation that could be applied with the fingers once daily and stored at room temperature for as long as 18 months. One product (clindamycin phosphate gel) combined all five of the preferred attributes, a preference confirmed by the simulated product rankings. These findings of the conjoint analysis are consistent with the safety profiles and the results of the traditional questionnaire.