With the increasing double burden of communicable and non-communicable diseases (NCDs) in sub-Saharan Africa, health systems require new approaches to organise and deliver services for patients requiring long-term care. There is increasing recognition of the need to integrate health services, with evidence supporting integration of HIV and NCD services through the reorganisation of health system inputs, across system levels. This study investigates current practices of delivering and implementing integrated care for chronically-ill patients in rural Malawi, focusing on the primary level.