Thirty three consecutive patients infected by human immunodeficiency virus type 1 (HIV1) with persistent diarrhoea which remained undiagnosed after microbiological examination of six stool samples and rectal histology were investigated for malabsorption. All had xylose and Schilling tests, distal duodenal biopsy, comprehensive barium studies, microbiological examination of six further stool samples, and repeat rectal histology. A microbiological or histological diagnosis of infection was made in 12 patients (multiple organisms in three). Cryptosporidia were identified on five occasions, cytomegalovirus on four, Giardia lamblia on two, and herpes simplex, Campylobacter jejuni, Salmonella enteritidis, and Entamoeba histolytica once each. No organism was found when weight loss was less than 5 kg or stool volume less than 400 ml/day (n = 9). Pathogens were identified in nine of 13 patients (69%) with weight loss greater than 10 kg and stool volume more than 800 ml/day. Barium studies were normal except for ileal flocculation in two patients with cryptosporidiosis. Evidence for malabsorption existed in 24 patients--impaired xylose absorption (n = 19) and abnormal Schilling test (n = 21). Of the patients with a severely abnormal Schilling test, a pathogen was identified in 11 (79%) (including all five with cryptosporidia, and two of the patients with only moderate diarrhoea and weight loss). A simple scoring system based on degree of weight loss and Schilling test result may help to identify the HIV positive patient with seemingly pathogen-negative diarrhoea in whom further investigations are likely to show a specific cause.