Enteric pathogens were determined from stools of 273 children aged less than 5 years at Kenyatta National Hospital (KNH), 43.6% (119/273) of whom were malnourished according to the Wellcome criteria. Rotavirus was detected by ELISA test, Salmonella, Shigella and E. coli by culture on MacConkey and Salmonella-Shigella agar at 37 degrees C overnight and Campylobacter on Skirrow's selective media at 42 degrees C for 48 hrs. These were identified by biochemical tests and serotyping using specific antisera. Whereas isolation rate for Campylobacter (0.0% vs 5.0%, p = 0.006), well malnourished ETEC-LT (0.6% vs 5.0%, p = 0.003) and T. hominis (0.0% vs 3.4%, p = 0.03) was higher in the malnourished children, EPEC (30.5% vs 10.1%, p < 0.001) and Salmonella+ETEC-LT (7.8% vs 1.7%, p = 0.02) was higher in children. The other enteric pathogens were equally isolated from normal and malnourished children. A larger proportion of malnourished children had diarrhoea of unknown aetiology compared to the well nourished (26.6% vs 50.4%, p < 0.001). Campylobacter and T. hominis may be opportunistic infections due to immuno-suppression in malnutrition. Diarrhoea of unknown aetiology may be due to aetiological agents that were not determined in this study.