BACKGROUND: Despite its contribution to global disease burden, diarrhoeal disease is still a relatively neglected area for research funding, especially in low-income country settings. The SNOWS consortium (Scientists Networked for Outcomes from Water and Sanitation) is funded by the Wellcome Trust under an initiative to build the necessary research skills in Africa. This paper focuses on the research training needs of the consortium as identified during the first three years of the project. METHODS: We reviewed the reports of two needs assessments. The first was a detailed needs assessment led by one northern partner, with follow-up visits which included reciprocal representation from the African universities. The second assessment, led by another northern partner, focused primarily on training needs. The reports from both needs assessments were read and stated needs were extracted and summarised. RESULTS: Key common issues identified in both assessments were supervisory skills, applications for external research funding, research management, and writing for publication in the peer-reviewed scientific literature. The bureaucratisation of university processes and inconsistencies through administration processes also caused problems. The lack of specialist laboratory equipment presented difficulties, particularly of inaccessibility through a lack of skilled staff for operation and maintenance, and of a budget provision for repairs and running costs. The lack of taught PhD modules and of research training methods also caused problems. Institutionally, there were often no mechanisms for identifying funding opportunities. On the other hand, grantees were often unable to understand or comply with the funders' financial and reporting requirements and were not supported by their institution. Skills in staff recruitment, retention, and performance were poor, as were performance in proposal and paper writing. The requirements for ethical clearance were often not known and governance issues not understood, particularly those required by funders. CONCLUSIONS: SNOWS believes that working with African universities to develop networks that support African-led research driven by the local context is an effective approach to develop and retain research skills needed to change policy and practice in water, sanitation, and hygiene in Africa.