From the 1950s until 1979 malaria control in Afghanistan was implemented through a vertical programme managed by the government, but little of the original programme remained functional by the early 1990s. Delivery of basic health care including malaria diagnosis and treatment was done by non-governmental organisations (NGOs) and UN agencies, which organised cross-border operations from Pakistan and Iran and placed much less emphasis on vertical programming. From 1992 the situation in the east of Afghanistan became stable enough to allow the establishment of a network of NGO-supported clinics and to introduce standardised training and monitoring of microscopists and clinical staff, coordinated by a lead agency specialising in malaria. After the collapse of the Taliban in 2001 and the subsequent establishment of an interim government, the first steps in health-system rehabilitation have been taken. The gradual integration of malaria control into routine health-care delivery is planned. This process should be guided by the knowledge and experience gained during the complex emergency and a focus on malaria should be maintained until the disease is brought under control.