Potential endpoints for blood stage malaria vaccine efficacy trials include uncomplicated malaria disease, which is hard to differentiate from other febrile illnesses, and mortality, which requires prohibitively large sample sizes. Strictly defined severe malaria predicts malaria-associated mortality where case fatality rates are known. To assess the suitability of severe malaria as a trial endpoint, we conducted a census in 1999 and measured the incidence of severe malaria from 1999 to 2001 in Bandiagara, Mali. The annual incidence of severe malaria in children <6 years of age was 2.3% (n = 2,284) yielding an estimated sample size of 4,580 for a vaccine trial designed to detect 50% efficacy with 80% power at P = 0.05 with 5% loss to follow-up. A trial using severe malaria as an endpoint in this setting would thus require expanding the study population or the length of the trial. This approach may be useful in assessing the suitability of potential sites for malaria vaccine trials.