Recently, there has been a major increase in financial support for malaria control. Most of these funds have, appropriately, been spent on the tools needed for effective prevention and treatment of malaria such as insecticide-treated bed nets, indoor residual spraying and artemisinin combination therapy. There has been less investment in the training of the scientists from malaria-endemic countries needed to support these large and increasingly complex malaria control programmes, especially in Africa. In 2000, with support from the Bill & Melinda Gates Foundation, the Gates Malaria Partnership was established to support postgraduate training of African scientists wishing to pursue a career in malaria research. The programme had three research capacity development components: a PhD fellowship programme, a postdoctoral fellowship programme and a laboratory infrastructure programme. During an 8-year period, 36 African PhD students and six postdoctoral fellows were supported, and two research laboratories were built in Tanzania. Some of the lessons learnt during this project--such as the need to improve PhD supervision in African universities and to provide better support for postdoctoral fellows--are now being applied to a successor malaria research capacity development programme, the Malaria Capacity Development Consortium, and may be of interest to other groups involved in improving postgraduate training in health sciences in African universities.