OBJECTIVES: Functional gastrointestinal disorder is common worldwide and a healthcare burden for many individuals. Functional dyspepsia and motility disorder can be extremely disabling. The aim of this study was to identify and weight the patient’s relevant decision criteria with regard to drug treatment of functional dyspepsia and motility disorders. Treatment characteristics such as the type of drug, onset of action, reduction of symptoms and side effects were to be examined in order to evaluate the patient preferences. METHODS: The literature review and nine qualitative interviews revealed eight patient-relevant treatment attributes. A discrete choice experiment (DCE) was used to rank the identified treatment characteristics. The DCE was conducted using a fractional-factorial-design (Ngene) and the statistical data analysis used random effect logit and latent class models for subgroup identification. RESULTS: In total N=1096 patients with functional dyspepsia or motility disorder participated in the computer-assisted personal interviews. The estimation revealed a clear dominance for a reduction of “stomach cramps” (coef.:3,01) and “epigastric pain” (coef.:2.98), followed by the reduction of “acid reflux/indigestion” (coef.:2.06), “time to onset of action” (coef.:1.57) and reduction of “feeling of fullness” (coef.:1.46).  The side effects “diarrhea” (coef.:1.20) and “headache” (coef.:1.05) as well as the “type of drug” was less important for participants (coef.:0.17). CONCLUSIONS: The reduction of symptoms like cramps and pain were identified as key patient-relevant characteristics. The sole consideration of these criteria is not sufficient from the patients’ perspective as multiple criteria are important. Subgroup analysis revealed that there are two population groups showing different preferences for the evaluated treatment characteristics. For one sub-sample the onset of action and side effects of a treatment are more important than a reduction of symptoms. The results inform decision makers on how much a decision criteria affects the potential treatment decision from a patient’s perspective.