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As a result of various public health crises, expertise in health risk assessment in France has become the responsibility of autonomous state agencies. However, practice shows that despite the institutional separation of expertise and decision-making, the link between health risk assessment and the management of health risks by the public authorities remains ambiguous. Tensions have emerged between the state and the various agencies responsible for providing expertise, especially in cases where agencies make recommendations on procedures and protocols. In addition, while a significant number of regulations have been designed to protect the independence of experts in the health sector, their implementation raises a wide range of practical issues. The number and nature of the common interests of experts and professionals in the health sector complicate the identification and management of potential conflicts of interest. Collaboration between expert bodies only partly compensates for these difficulties. Finally, the involvement of ’stakeholders’ concerned by the results of expertise have sparked a debate that remains unresolved. While some view it as a source of greater knowledge, others have seen the participation of ’lay’ experts as a threat to the quality and impartiality of expertise. Regardless of the preferred approach, recent events show that stakeholders play a key role in health risk monitoring and assessment.