In recent years a succession of health emergencies connected with the threat of new, possibly global, infectious diseases has stimulated the attention of the mass media, the scientific community, and international public opinion, setting a tough test for the institutions whose job is to manage the risks. On the basis of experience in the fields of AIDS, BSE, SARS and bird flu, this study discusses the strong and weak points of governance procedures for health risks. In particular, the paper illustrates how risk management can be improved by adopting practices and procedures which actively involve the public in dealing with the emergency, by taking a transparent and accessible approach to communication with the public (including the provision of information about the risks) and by fostering the unrestricted exchange of scientific knowledge among researchers. Lastly, the text shows how the analysis of these themes provides starting points for understanding the crisis in the current relationship between science and society.