A healthy microbiota cannot be defined in general, as individual and interindividual variations are considerable. In the future, it may be possible to characterize a healthy microbiota on an individual level related to geographical location, diet and genetic factors. Deviations in microbiota are nevertheless often easier to identify, especially when they relate to particular disease risks, for example obesity and metabolic diseases or allergies. Microbiota development commences earlier than previously thought and may be initiated at fertilization and continue through pregnancy. The establishment of an intestinal microbial community appears to be a stepwise controlled process covering the first year of life. Factors affecting its compositional development are associated with genetic and environmental factors; mother’s health status, lifestyle and microbiota; geographic location and antibiotic treatments among others. Differences in microbiota composition in the early stages of life can be correlated with various microbial functional properties and differences in the production of microbial metabolites such as short-chain fatty acids or polyamines. Several studies show that these differences have an impact on gastrointestinal development, with consequences for later health. Alterations in the compositional development and activity of microbes may be partially responsible for the programming of the infant immune system and later health. Vaginal delivery, breastfeeding and limiting the perinatal influence to the use of antibiotics should be recommended for the promotion of normal microbiota development.