The intestinal flora of breast-fed infants differs from that of formula-fed infants. It is thought that this difference in flora may be one important reason why breast-fed babies suffer less from gastrointestinal disease. Differences in intestinal flora are reflected in the profile of faecal short chain fatty acids (SCFA). Very little is known about faecal concentrations of SCFA in babies fed breast milk or infant formula. In this study, faecal SCFA were measured in babies at two and four weeks of age who had been either exclusively breast fed or bottle fed from birth. There was no significant difference in total faecal SCFA concentrations between breast-fed and formula-fed babies when lactate was included. The formula-fed group, however, had less lactic acid and higher concentrations of propionic and n-butyric acids than breast-fed babies. Very few babies had significant levels of n-butyric acid, although this SCFA is believed to be important for the health of the colonic mucosa of adults.