With the development of antimalarial drug resistance in the Greater Mekong Subregion, it is especially important to monitor cases – even in low-intensity transmission areas – in order to contain, and eventually eliminate, the resistant parasite. The RAI ICC2 project targets border areas of Cambodia and Thailand to: i) map hotspots of infection and identify sub-populations with the highest risk of infection as well as under-utilisation of current malaria control methods; ii) target identified hotspots with tailored interventions to diagnose and treat both clinical cases and asymptomatic carriers; iii) increase preventive behaviours through use of behaviour change communication as well as information, education and communication; and iv) improve cross-border data sharing and collaboration. Interventions include active case detection methods and intensified case-finding (ICF) at border points and in hotspots, piloting novel alert systems both at community and private provider levels, and the delivery of behaviour change communication initiatives. Efforts build upon current in-country components of the Regional Artemisinin Initiative (RAI) and other programmes which are currently ongoing in the region by directing resources to those most in need. Intervention packages are tailored to suit each region according to local resources and capacity in order to ensure sustainability and cost-effectiveness.