Low income countries in Southeast Asia are in a region at risk of emerging infectious diseases, notably SARS, H5N1 influenza and H1N1 influenza. Efforts have focused largely upon early outbreak response, though with the emergence of pandemic influenza, countries in the region are having to prepare to implement mitigation measures. We review the challenges for strategy and operation faced by two low income countries, Cambodia and Lao People's Democratic Republic (PDR), and highlight successes in planing and implementation to date as well as identifying needs and challenge that may hinder the future effectiveness of control measures.