Enteric infections, impaired digestion, loss of villous cells, and poor absorption of fat may lead to presence of neutral fat in stool, particularly in children with diarrhoea. We aimed to examine the association between presence of neutral fat in stool and aetiology of diarrhoea and nutritional status of the patients at different age groups. A total of 13,171 patients aged 5 days-106 years enrolled in the Diarrhoeal Disease Surveillance System of the Dhaka Hospital of ICDDR,B during 1996-2001 were studied. Presence of neutral fat in faecal specimens, aetiology of diarrhoea, and nutritional status in children below 5 years of age were determined and analysed. Of the total study individuals, 7,671 (58%) had neutral fat in their faecal specimens. Neutral fat was more frequently present in faeces of individuals infected with rotavirus in all age groups or in enterotoxigenic E. coli (ETEC) infection in children 0-23 months old while compared with those who did not have these infections (p=0.005, p=0.014, respectively). Neutral fat was less frequently (p<0.001) present in malnourished 0-23 months old children. Presence of neutral fat in the stool in diarrhoea due to rotavirus and in young childhood ETEC diarrhoea signifies compromised gastrointestinal function due to these infections. The mechanism of persistence of neutral fat in the stool of such patients, and its nutritional and clinical implications require further studies.