Regional policies and programmes on communicable disease prevention and control are becoming an important component of global public health. In a comparative fashion, we examined the situation in the European and Southeast Asian contexts, with a focus on the underlying institutional and political backgrounds underpinning the regionalisation of planning and interventions. Our findings document the emergence of two distinctive models of regional integration. While in Europe there is a process of institutionalisation and centralisation, in Southeast Asia the landscape of regional cooperation is characterised by the proliferation of many provisional projects, based on loose agreements and a decentralised structure that emphasises the initiative and sense of ownership of member countries. These two approaches, we conclude, reflect wider differences of political culture between supranational integration in Europe and intergovernmental agreements in Southeast Asia.