Background. Infection in neutropenic children is a major cause of morbidity and mortality in children treated for cancer. In developing countries, children with cancer are often malnourished at diagnosis. In Blantyre, Malawi, children with Burkitt lymphoma are treated with a local protocol with limited toxicity. The aim of this study was to evaluate the incidence and outcome of febrile neutropenia during this treatment and the association with malnutrition at diagnosis. Methods. We documented nutritional status, febrile and/or neutropenic episodes, antibiotic therapy and short term outcome of all children with Burkitt lymphoma treated according to the local protocol and admitted from January 2007 to March 2008. Results. Fifty eight (69%) of 84 patients were acutely malnourished at diagnosis with an arm muscle area (AMA) below the 5 th percentile. Malnutrition at diagnosis was associated with a significantly higher rate of profound neutropenia. This association remained significant (OR 12; 95% C.I. 1.5 - infinitely; P = 0.012) after control for clinical stage of disease, bone marrow involvement and HIV infection which are possible confounders. All patients with profound neutropenia, prolonged neutropenia and treatment related deaths were malnourished at diagnosis. Four (4.9%) of 81 patients died of treatment related causes; three of them due to a Gram negative septicaemia. Conclusion. Acute malnutrition at diagnosis is associated with significantly more treatment related profound neutropenia. The intensity of chemotherapeutic regimens has to be adapted to the level of available supportive care and patients' nutritional status and tolerance to avoid unacceptable morbidity and mortality. This local treatment protocol for Burkitt lymphoma has a treatment related mortality of 5% in patients in Malawi.