To investigate the effects of mode of delivery and of necrotising enterocolitis on the faecal microflora, 140 infants born before 33 weeks of gestation were followed up for symptoms of necrotising enterocolitis. Stool samples for gas-liquid chromatography and culture were collected twice weekly, and, when necrotising enterocolitis was suspected, for 2 months. For each infant with necrotising enterocolitis (n=21), two control infants matched for birth weight and gestational age were selected from the remaining study population. In gas-liquid chromatography analysis, the faecal bacterial microflora of infants born via caesarean section differed significantly from the gut microflora of those born via the vaginal route. The intestinal microflora showed a significant alteration in the necrotising enterocolitis group at time of diagnosis. At the onset of necrotising enterocolitis, faecal colonisation with Enterococcus species and Candida albicans was significantly more frequent in symptomatic infants than in controls. In infants with positive blood cultures and positive intestinal biopsy cultures, concomitant stool samples revealed the same microbial pathogens. In conclusion, the intestinal microbial colonisation in preterm infants born by caesarean section differs from that in preterm infants born via the vaginal route. A significant change in faecal microbial colonisation seems to occur at the onset of necrotising enterocolitis. Pathogens detected in the stools at that time might have a causative role in the development of the disease.