The aim of this study was to test the congruence of patients' health valuations and physicians' treatment goals for the rehabilitation of chronically ill patients. In addition, patient characteristics associated with greater or less congruence were to be determined. In a questionnaire study, patients' health valuations and physicians' goals were assessed in three chronic conditions [breast cancer (BC), chronic ischemic heart disease (CIHD), and chronic back pain (CBP)] using a ranking method. Sociodemographic variables and health-related quality of life were assessed as patient-related factors that influence congruence. Congruence was determined at the group (Spearman's rho) and individual levels (percentage of congruence). Patient-related influencing factors were calculated after a simple imputation using multiple logistic regression analysis. At the group level, there were often only low correlations. The mean percentage of congruence was 34.7% (BC), 48.5% (CIHD), and 31.9% (CBP). Patients with BC or CIHD who have a higher level of education showed greater congruence. Our results indicate some high discrepancy rates between physicians' treatment goals and patients' health valuations. It is possible that patients have preferences that do not correspond well with realistic rehabilitation goals or that physicians do not take patients' individual health valuations sufficiently into consideration when setting goals.