The intestinal microbiota is an important factor for proper growth and development from birth to adulthood. Bacterial colonization initiates direct contact of the newborn with the mother’s vaginal, intestinal, and skin microbiota. The composition of the microbiota depends on whether the baby was born by caesarean section or vaginal route, was breastfed or fed with milk formulas, was receiving antibiotics, or wich gestational age was at birth. The composition of microbiota also depends on the socioeconomic status of the mother and the geographical location. It has been shown that qualitative and quantitative changes in the microbiota contribute to changes in the activation of the mucosal immune system with the consequent development of intraintestinal and extraintestinal diseases. Intestinal dysbiosis during neonatal and infant period was present in children who later developed necrotizing enterocolitis, inflammatory bowel disease, celiac disease, constipation and diarrhea, but also extraintestinal diseases such as obesity, allergic diseases and neurodevelopmental disorders. Probiotics and prebiotics can promote changes in the composition of the microbiota in order to achieve various health benefits. The mechanism of action of probiotics is complex and includes regulation of gene expression of pro-inflammatory genes, production of short-chain fatty acids that suppress the growth of pathogenic bacteria, support the mucosal epithelial barrier and regulation of cellular immunity. By correcting the intestinal microbiota, they have a preventive and therapeutic effect on the previously mentioned pediatric gastrointestinal and extraintestinal diseases