Clinical ethics committees (CECs) have been developing in many countries since the 1980s, more recently in the transitional countries in Eastern Europe. With their increasing profile they are now faced with a range of questions and challenges regarding their position within the health care organizations in which they are situated: Should CECs be independent bodies with a critical role towards institutional management, or should they be an integral part of the hospital organization? In this paper, we discuss the organizational context in which CECs function in Europe focusing on five aspects. We conclude that in Europe clinical ethics committees need to maintain a critical independence while generating acceptance of the CEC and its potential benefit to both individuals and the organization. CECs, perhaps particularly in transitional countries, must counter the charge of "alibi ethics". CECs must define their contribution to in-house quality management in their respective health care organization, clarifying how ethical reflection on various levels serves the hospital and patient care in general. This last challenge is made more difficult by lack of consensus about appropriate quality outcomes for CECs internationally. These are daunting challenges, but the fact that CECs continue to develop suggests that we should make the effort to overcome them. We believe there is a need for further research that specifically addresses some of the institutional challenges facing CECs.