Aim The development of the gut microbiota occurs primarily during infancy, and growing evidence has emphasised its positive role and implications for human health. The aim of this review was to provide essential knowledge about the gut microbiota and to describe and highlight the importance of the factors that influence the gut microbiota in early life and their potential harmful effects later in life. Methods The European Paediatric Association, the Union of the National European Paediatric Societies and Associations, convened a panel of independent European experts to summarise the research on microbiota for general paediatricians. They used PubMed and the Cochrane Library to identify studies published in English up to June 2018. Results A number of clinical conditions can disrupt the development of a stable gut microbiota. Changes in the microbiome have been documented in many chronic diseases, mainly immune-mediated gastrointestinal and liver diseases, and distinct patterns have been associated with each specific disease. The gut microbiota can be positively modulated with probiotics, prebiotics, synbiotics, paraprobiotics and postbiotics. Conclusion Paediatricians can play a key role in preventing harmful events that could permanently influence the composition and/or function of the gut microbiota. Various treatment strategies can be used.