The rationale for supplementing an infant formula with prebiotics is to obtain a bifidogenic effect and the implied advantages of a ‘breast-fed-like’ flora. So far, the bifidogenic effect of oligofructose and inulin has been demonstrated in animals and in adults, of oligofructose in infants and toddlers and of a longchain inulin (10 %) and galactooligosaccharide (90 %) mixture in term and preterm infants. The addition of prebiotics to infant formula softens stools but other putative effects remain to be demonstrated. Studies published post marketing show that infants fed a long-chain inulin/galactooligosaccharide mixture (0·8 g/dl) in formula grow normally and have no side-effects. The addition of the same mixture at a concentration of 0·8 g/dl to infant formula was therefore recognized as safe by the European Commission in 2001 but follow-up studies were recommended. It is thought that a bifidogenic effect is beneficial for the infant host. The rising incidence in allergy during the first year of life may justify the attempts to modulate the infant's flora. Comfort issues should not be confused with morbidity and are likely to be multifactorial. The functional effects of prebiotics on infant health need further study in controlled intervention trials.