Background: In Germany, EBM is increasingly used to standardize medical decision making and treatment. It is recognized increasingly that trustful physician-patient interactions are of central importance in effective medical care for chronically ill patients. However, EBM as practiced in Germany cannot accommodate concepts that resist quantitative analysis such as physicians’ experience or patients’ preferences. Objectives: To evaluate a) the present situation of medical practice in Germany by determining physicians’ actual reasons for selecting a specific treatment for their patient, and b) by asking patients for reasons of treatment satisfaction. Methods: A telephone survey was conducted with practicing physicians (n = 313) to evaluate reasons for selecting treatments and attitudes towards EBM. Five specific indications, i.e. low back pain, rheumatoid arthritis, asthma/COPD, diabetes mellitus Type 2, and schizophrenia, were selected to investigate the prescription approaches of physicians with respect to the published treatment guidelines and EBM assessments. The physicians’ view was complemented by a patient telephone survey (n = 365) evaluating treatment satisfaction in these indications. Results: Physicians use information from multiple sources to base their therapeutic decisions on, but rely predominantly on their own experience. GPs appear to be more critical towards EBM than specialists. Results from the patient survey reveal that patients expect that their individual needs as well as their personal experiences with a given therapy are being considered by their physician and that a dialogue between patient and physician shall guide the course of treatment aiming at optimal balance between EBM derived therapy effectiveness and individual, patient-based assessment of a particular treatment approach with respect to entirely subjective impressions and judgements. Conclusions: Evaluations of medical interventions based entirely on EBM assessments as presently practiced in Germany have limited relevance for treatment decisions made by practicing physicians. Furthermore, benefit assessment of medications and health technologies, when used as a measure of treatment satisfaction, requires additional consideration of patient-oriented criteria to achieve the desired target of adequate patient care. Therefore, the concept of patient-based medicine is proposed to embed current EBM practice into a more patient-focused approach to increase physicians’ acceptance of EBM.