OBJECTIVES: This study was designed to capture patient preferences for different aspects of Crohn’s disease (CD) treatment for people with CD in Spain. METHODS: Main attributes of CD flare-up treatment were determined from a review of the literature and consultations with medical experts and patients. The discrete choice experiment (DCE) included 5 attributes: type of drug administration, disease control, aesthetic effects, mild-to-moderate adverse events and serious adverse events, plus a cost attribute in order to estimate willingness to pay (WTP) for improvements in attribute levels. A pilot study with 20 patients was carried forward to identify areas of misunderstanding. One hundred sixty-eight patients with a diagnosis of Crohn’s disease were presented with pairs of hypothetical treatment profiles with varied levels of adverse events, disease control, type of administration and cost. Questions were also included to collect socio-demographic data (including income). Data were analyzed using a random effects probit model. RESULTS: All attributes had the expected polarity and all were significant predictors of choice, i.e. participants showed a preference for less severe adverse effects, greater flare control and less cost. Patients were WTP for a reduction of a 10% in the probability of experiencing: serious adverse events, €1443.53/month; aesthetic adverse events, €54.50/month and mild-to-moderate adverse events, €3.86/month and €135.06/month for an increase of a 10% in the probability of obtaining a clinical response. Patients were also willing to pay €146.91/month and €228.66/month to have their treatment administered orally rather than with an injection or an infusion respectively. CONCLUSIONS: Patients with CD have well-defined preferences among treatment attributes and are willing to accept tradeoffs among attributes. Study participants indicated that they are willing to accept elevated mild-to-moderate or aesthetic adverse event risks in exchange for clinical efficacy. The perspective of the patients should be taken into account when making treatment decisions.