Human milk is the gold standard for nourishment of early infants because it contains a number of bioactive components, such as human milk oligosaccharides (HMOs). The high concentration and structural diversity of HMOs are unique to humans. HMOs are a group of complex and diverse glycans that are resistant to gastrointestinal digestion and reach the infant colon as the first prebiotics. N-acetyl-glucosamine containing oligosaccharides were first identified 50 years ago as the ‘bifidus factor’, a selective growth substrate for intestinal bifidobacteria, thus providing a conceptual basis for HMO-specific bifidogenic activity. Bifidobacterial species are the main utilisers of HMOs in the gastrointestinal tract and represent the dominant microbiota of breast-fed infants, and they may play an important role in maintaining the general health of newborn children. Oligosaccharides are also known to directly interact with the surface of pathogenic bacteria, and various oligosaccharides in milk are believed to inhibit the binding of pathogens and toxins to host cell receptors. Furthermore, HMOs are thought to contribute to the development of infant intestine and brain. Oligosaccharides currently added to infant formula are structurally different from the oligosaccharides naturally occurring in human milk and, therefore, they are unlikely to mimic some of the structure-specific effects. In this review, we describe how HMOs can modulate gut microbiota. This article summarises information up to date about the relationship between the intestinal microbiota and HMOs, and other possible indirect effects of HMOs on intestinal environment.