Background: In Germany, evidence-based medicine (EBM) is increasingly used to standardise medical decision making and patient treatment. As a consequence this development leads to a shift of influence in health care decision making from physicians to institutional representatives, payers and health care policy makers. However, EBM's practical role in day-to-day patient care is less clearly defined. Aim: The aim of this study was to evaluate a potential difference between EBM assessment of therapy benefits and empirical judgment by prescribing physicians and their patients. Methods: Interviews were conducted with practising physicians to evaluate reasons for selecting treatments and attitudes towards EBM. The physicians' view was complemented by a patient telephone survey evaluating treatment satisfaction in selected indications. Results: The findings of the physician survey suggest that many general practitioners (GPs) as well as specialized practitioners in Germany do not share EBM's paramount concern with clinical effectiveness, but see it as one aspect in a wider concept that also includes patient-oriented concerns such as patient satisfaction, minimal infliction on patients' day-to-day life and incompatibility with other needs or treatments. Another important finding is the notion that EBM is misused by health care policy aimed at restricting clinical practice options by focussing entirely on clinical effectiveness without considering the complex physician-patient interaction required for implementing a successful treatment process. Results from the patient survey reveal the patients' expectation that their individual needs as well as their personal experiences with a given therapy are being considered and that a dialogue between patient and physician shall guide the course of treatment with the aim of finding an optimal balance between EBM-derived therapy effectiveness and individual, patient-based assessment of a particular treatment approach with respect to entirely subjective impressions and judgments. Discussion: The results of this study demonstrate that practising physicians consider not only evidence-based information, but also patient-oriented criteria to achieve adequate patient care and compliance. Patients wish to discuss disease and personal therapy experiences with their physician and emphasize their intention to actively participate in the treatment process. Therefore, the concept of patient-based medicine is proposed as an extension of current EBM practice in everyday patient treatment as well as for regulatory decision making regarding health care services. © 2008 Springer-Verlag.