A WHO methodology is used for the first time to estimate the burden of disease directly associated with incomplete water and sanitation provision in refugee camps in sub-Saharan African countries. In refugee camps of seven countries, containing just fewer than 1 million people in 2005, there were 132,000 cases of diarrhoea and over 280,000 reported cases of malaria attributable to incomplete water and sanitation provision. In the period from 2005 to 2007 1,400 deaths were estimated to be directly attributable to incomplete water and sanitation alone in refugee camps in Ethiopia, Kenya and Tanzania. A comparison with national morbidity estimates from WHO shows that although diarrhoea estimates in the camps are often higher, mortality estimates are generally much lower, which may reflect on more ready access to medical aid within refugee camps. Despite the many limitations, these estimates highlight the burden of disease connected to incomplete water and sanitation provision in refugee settings and can assist resource managers to identify camps requiring specific interventions. Additionally the results reinforce the importance of increasing dialogue between the water, sanitation and health sectors and underline the fact that efforts to reduce refugee morbidity would be greatly enhanced by strengthening water and sanitation provision.