Effective control of asthma requires regular preventive medication. Poor medication adherence suggests that patient preferences for medications may differ from the concerns of the prescribing clinicians. This study investigated patient preferences for preventive medications across symptom control, daily activities, medication side-effects, convenience and costs, using a discrete choice experiment embedded in a randomized clinical trial involving patients with mild moderate persistent asthma. The present data were collected after patients had received 6 weeks treatment with one of two drugs. Three choice options were presented, to continue with the current drug, to change to an alternative, hypothetical drug, or to take no preventive medication. Analysis used random parameter multinomial logit. Most respondents chose to continue with their current drug in most choice situations but this tendency differed depending on which medication they had been allocated. Respondents valued their ability to participate in usual daily activities and sport, preferred minimal symptoms, and were less likely to choose drugs with side-effects. Cost was also significant, but other convenience attributes were not. Demographic characteristics did not improve the model fit. This study illustrates how discrete choice experiments may be embedded in a clinical trial to provide insights into patient preferences.