The international community, comprised of national governments, multilateral agencies and civil society organisations, has recently negotiated a set of 17 sustainable development goals (SDGs) and 169 targets to replace the Millennium Development Goals, which expired in 2015. For progress in implementing the SDGs, ensuring policy coherence for sustainable development will be essential. We conducted a health impact assessment to identify potential incoherences between contemporary regional trade agreements (RTAs) and nutrition and health-related SDGs. Our findings suggest that obligations in RTAs may conflict with several of the SDGs. Areas of policy incoherence include the spread of unhealthy commodities, threats to equitable access to essential health services, medicines and vaccines, and reduced government regulatory flexibility. Scenarios for future incoherence are identified, with recommendations for how these can be avoided or mitigated. While recognising that governments have multiple policy objectives that may not always be coherent, we contend that states implementing the SDGs must give greater attention to ensure that binding trade agreements do not undermine the achievement of SDG targets.