Modern trade negotiations have delivered a plethora of bilateral and regional preferential trade agreements (PTAs), which involve considerable risk to public health, thus placing demands on governments to strengthen administrative regulatory capacities in regard to the negotiation, implementation and on-going management of PTAs. In terms of risk management, the administrative regulatory capacity requisite for appropriate negotiation of PTAs is different to that for the implementation or on-going management of PTAs, but at all stages the capacity needed is expensive, skill-intensive and requires considerable infrastructure, which smaller and poorer states especially struggle to find. It is also a task generally underestimated. If states do not find ways to increase their capacities then PTAs are likely to become much greater drivers of health inequities. Developing countries especially struggle to find this capacity. In this article we set out the importance of administrative regulatory capacity and coordination to manage the risks to public health associated with PTAs, and suggest ways countries can improve their capacity.