The development of the bacterial flora of neonates with congenital abnormalities of the gastro-intestinal tract was studied in 31 infants during the first 10 days of life. Specimens were collected from the umbilicus, mouth and gastro-intestinal tract on the pre-operative day, at operation and on post-operative days 1, 2, 3, 5, 7 and 10. Bacteria were isolated semi-quantitatively on a variety of plain and selective media and identified by conventional methods.Staphylococcus albus was the predominant species isolated from the umbilicus; it was recovered from 24 of the 31 babies. The viridans group of streptococci and Streptococcus salivarius were the commonest species isolated from the mouth; there were no differences between the babies with different abnormalities and treatment with antibiotics had no effect on the bacterial flora. Ten babies were colonized by each species on the pre-operative day, and 25 and 19 respectively by the tenth post-operative day. Anaerobic gram-positive cocci were the predominant oral anaerobes. Bacteria were not isolated from the rectal swabs of babies with tracheo-oesophageal fistula (TOF) or small bowel atresia on the pre-operative days. Post-operatively the predominant faecal isolates from babies with TOF were Str. faecalis, Escherichia coli and Clostridium perfringens. About 80% of the babies with small bowel atresia were colonized by Str. faecalis and Bacteroides vulgatus, 60% each by E. coli, Klebsiella aerogenes and Str. faecium. The five babies with necrotizing enterocolitis were colonized by Str. faecalis, E. coli, Cl. perfringens and Cl. difficile; Bacteroides spp. were not recovered from any of them. The commonest facultative species recovered from babies with large bowel obstruction were Str. faecalis and E. coli. B. vulgatus, Cl. perfringens and Bifidobacterium spp. were the commonest anaerobes and anaerobes outnumbered aerobes. No significant isolates were recovered from the wound swabs and none of the babies developed post-surgical sepsis.