OBJECTIVES: Patient preferences for alternative treatments may be affected by health status and experience with the treatment. Randomized Clinical Trials (RCTs) offer a unique opportunity to collect preference data while controlling for patient experience. METHODS: Patients with Type II diabetes in a large US RCT answered a series of stated preference (conjoint format) questions regarding attributes of alternative insulin therapies. All patients are insulin-naïve and take insulin as part of the trial. Preference data is collected before the patient begins insulin, after 3 months, and after 6 months of insulin therapy. Insulin attributes include the frequency of insulin injections, method of injection (syringe or pen), glucose control and frequency of hypoglycemia. Personal health data such as glucose control are collected at each administration of the stated preference survey. RESULTS: Preferences are analyzed in an ordered probit panel model that controls for individual health status. Insulin administration attributes have the largest importance scores. The importance score of the insulin injection frequency attribute decreases during the later observation points. While few patients experience nighttime hypoglycemia, this attribute is significant and has a larger importance score than glucose control. CONCLUSIONS: Patient experience significantly affects patient preferences and the derived pharmacoeconomic measures and should be controlled in preference experiments. Results suggest that some insulin-naïve patients are more averse to insulin injections before they begin insulin therapy. Results also suggest that increased experience with diabetes control measures during the trial affects treatment preferences.