A study was undertaken in a central nutritional rehabilitation unit in southern Malawi to assess the impact of HIV infection on clinical presentation and case fatality rate. HIV seroprevalence in 250 severely malnourished children over 1 year of age was 34.4% and overall mortality was 28%. HIV infection was associated significantly more frequently with marasmus (62.2%) than with kwashiorkor (21.7%) (p < 0.0001). Breastfed children presenting with severe malnutrition were significantly more likely to be HIV-seropositive (p < 0.001). Clinical and radiological features were generally not helpful in distinguishing HIV-seropositive from HIV-seronegative children. The case fatality rate was significantly higher for HIV-seropositive children (RR 1.6 [95% CI 1.14-2.24]). The increasing difficulties of managing the growing impact of HIV infection on severely malnourished children in Malawi are discussed in the context of reduced support for nutritional rehabilitation units.