The purpose of this Special Issue, “Prebiotics and Probiotics”, is to focus on the importance of intestinal microbiota for human health and disease and the possibilities of influencing its composition and function with probiotics and prebiotics. The goal is to clarify that the microbiome in the maternal fetal and during pediatric age, as well as the immediate changes that occur as new microbes are acquired postnatally play major roles in subsequent health and disease. Rapidly developing technologies for multi-omic analyses and systems biology are shifting paradigms in both scientific knowledge and clinical care. Finally, the idea will be to provide health professionals with comprehensive, understandable and highly readable updated information on the intestinal microbiota, probiotics and prebiotics.