Objective. To examine parents' preferences for drug treatments and health outcomes in juvenile idiopathic arthritis (JIA) and identify demographic and health-related factors that significantly impact choice. Methods. A discrete choice experiment was conducted with 105 parents of children with JIA who were cared for by a rheumatologist at The Hospital for Sick Children in Canada. Attributes evaluated included "drug treatment," "child reported pain from arthritis," "participation in daily activities," "side effects," "days missed from school," and "cost to you." Multinomial logit regression was used to estimate the relative importance of each attribute level and interaction term. Results. Parents made tradeoffs between characteristics of the drug treatments and health outcomes. "Participation in daily activities" was the most important attribute, followed by "child reported pain from arthritis" and "cost to you." Parents of children with longer disease durations had stronger preferences for improved participation in daily activities, whereas parents of older JIA patients had stronger preferences for improved control of pain. Conclusion. Parents of children with JIA demonstrated strong preferences for treatments that reduce pain and improve daily functioning regardless of the associated side effects, level of responsibility required for drug administration, and days missed from school. Parents of children with longer disease durations and those who had been prescribed aggressive therapies had a greater preference for treatment effectiveness. These findings support the need for considering parental preferences in decisions regarding the choice of treatment for JIA.