Microflora of the gut was studied close to the onset of sporadic necrotizing enterocolitis (NEC) in neonates. Enteric flora in 25 babies with NEC differed from that in 23 matched controls. Bacteroides spp and lactobacilli were less common in babies with NEC compared with controls: 32 versus 61% (p = 0.03) and 12 versus 48% (p = 0.006), respectively. Clostridium perfringens was isolated from 40% of babies with NEC compared with 13% of controls (p = 0.03). It was present in 33% of babies with NEC aged less than 14 days but was not detected in control babies of the same age. The incidences of C. butyricum and C. difficile were similar in patients and controls. Colonization with C. perfringens in the absence of a protective barrier flora may be crucial in the pathogenesis of severe sudden onset NEC. Two potentially valuable marker factors to predict onset of this form of sporadic NEC are the use of fecal smears and estimation of fecal tryptic activity.