The World Health Organisation (WHO) and the World Organisation for Animal Health (OIE) have introduced normative and cognitive changes in response to the challenge of emerging infectious diseases (EIDs). These changes take the form of a paradigm shift from 'an international management of threats' towards 'a global governance of risks'. The distinction between these two paradigms is developed in this paper based on literature on public health policy and on risk sociology. Here, we suggest that risks differ from threats (or classical risks) by being uncertain, global and anticipated catastrophes. They require an alternative paradigm of risk governance based on precaution, transparency and participation. To demonstrate empirically this shift, the paper analysed the WHO and OIE's response to recent EIDs, and in particular bird flu (H5N1). With H5N1, these organisations have shown an unprecedented ambition to handle a 'prepandemic' virus; they have called for increased transparency from Member States on their epidemiologic status, and for the inclusion of a wider range of stakeholders into the task of epidemiologic surveillance. This paper shows that the WHO and the OIE framed EIDs as modern risks and handled them using the 'global risks governance' paradigm. In doing so, they seized the opportunity, in a competitive way, to legitimise a wider scope of intervention for themselves by revising their regulatory tools (the International Health Regulation and the Terrestrial Animal Health Code) and by extending the obligations of the Member States via their system of notifiable events. This shift raises the issue of the instrumentalisation of the paradigm of global risk governance. It questions States' sovereignty, and stakeholder's participation and it highlights the political potential of modern risks, the link with the production of knowledge and the activity of surveillance in a world at risk.