The application of Evidence-based Medicine (EbM) in clinical practice is characterised by different expectations shaped by the interests of the various players of the health care system. Ethical analysis of the medical ethicist anticipates such expectations, especially by giving consideration to potential negative outcomes for particular patient groups in order to identify systematic distortions and to avoid discrimination of patients concerning access to medical care. In this context, the adequacy of the basic evaluation criteria of EbM for different health conditions needs to be investigated, too. In addition possible conflicts of interest in practising EbM will have to be discussed openly with patients being involved in this process as well as in the development of evidence-based guidelines.