Since 2004 standard malaria treatment guidelines across Africa have universally changed to support the management of clinical malaria in formal, public health services with ACTs, representing one of the most significant policy changes in malaria. However, we have shown through facility-based studies in Kenya, Uganda, Zambia and Somalia that malaria case-management in the public sector remains characterized by a poor drug supply, inappropriate prescription practices, inadequate counselling of patients and a disregard of results of parasitological diagnosis aimed at reducing over-treatment.