The paper draws on the recent science and technology scholarship (STS) to criticise the dominant understanding of the role of science on which the existing system of transnational regulation is based. In particular, it employs the concept of epistemic subsidiarity suggested by Sheila Jasanoff to the science-based regulation in the EU to explain why the formal authority of the GMO regulators is crumbling, while some transnational regimes with no formal legal foundation flourish. It argues that to build their own authority, transnational regimes must not dismiss local concerns as ‘unscientific’ and ‘political’ but should themselves seek to take these concerns into account. The paper explores several ways in which this might be done in a multilevel system and concludes that instead of seeking to circumscribe the domains, we should strive to make their boundaries more porous.