There is evidence that an optimal match of patients' participation preferences improves health outcomes. Since it is unknown whether psychiatrists and neurologists can predict their patients' participation preferences we performed a cross-sectional survey involving N = 101 inpatients with schizophrenia/schizoaffective disorder and N = 102 inpatients with multiple sclerosis. Both patients and their physicians in charge were surveyed with respect to the patients' participation preferences, using the Autonomy Preference Index and a global estimate. Most patients wished to participate in medical decision making. Doctors performed poorly when predicting their individual patients' participation preferences and tended to overestimate their patients' participation preferences. A longer duration of the hospital stay did not improve the accuracy of doctors' estimates. Thus, neurologists and psychiatrists fail at predicting their patients' participation preferences accurately, which might challenge patients' treatment satisfaction. More attention in the consultation should be paid to patients' preferences.