This article tries to present a broad view on the values and ethical issues that are at stake in efforts to rationalize health policy on the basis of economic evaluations (like cost-effectiveness analysis) and randomly controlled clinical trials. Though such a rationalization is generally seen as an objective and 'value free' process, moral values often play a hidden role, not only in the production of 'evidence', but also in the way this evidence is used in policy making. For example, the definition of effectiveness of medical treatment or health care service is heavily dependent on dominant individual or social views about the goals of the particular treatment or service. There is also a concern that a reliance on EBM in health policy will occur at the expense of widely shared social values like equity and solidarity. Moreover, there is a concern that when economic considerations and rational procedures become more influential, various 'outside' groups third parties like insurance companies and policy makers will get a stronger influence on medical practice which may lead to a change in the patient-provider relationship. The authors conclude that social values and patient preference should be explicitly addressed when health policy making is based on economic and other scientific evidence.