AIM: To assess the clinical outcomes of a combined approach to the treatment of severe acute malnutrition in an area of high HIV prevalence using: (i) an initial inpatient phase, based on WHO guidelines and (ii) an outpatient recovery phase using ready-to-use therapeutic food. METHODS: An operational prospective cohort study implemented in a referral hospital in Southern Malawi between May 2003 and 2004. Patient outcomes were compared with international standards and with audits carried out during the year preceding the study. RESULTS: Inpatient mortality was 18% compared to 29% the previous year. Programme recovery rate was 58.1% compared to 45% the previous year. The overall programme mortality rate was 25.7%. Of the total known HIV seropositive children, 49.5% died. CONCLUSIONS: Inpatient mortality and cure rates improved compared to pre-study data but the overall mortality rate did not meet international standards. Additional interventions will be needed if these standards are to be achieved.