The microbiota living in the human gut has received tremendous attention within the last decade. A broad spectrum of high-prevalence pediatric diseases has been associated with alterations in gut microbiota (presented here in order of total number of publications on PubMed with the most prevalent diseases first): overweight and metabolism, Clostridium difficile infection, irritable bowel syndrome, inflammatory bowel disease (IBD), allergy, necrotizing enterocolitis, gut–brain axis disorders (e.g., autism, neurodevelopment, depression), malnutrition, celiac disease, 270asthma, and colic. Major scientific contributions with regard to microbiota have been published within the field of overweight/obesity and metabolism. This chapter focuses on the intestinal microbiota and its association with metabolic dysfunctions and pediatric overweight as well as elucidates recent research regarding the acquisition and development of the gut microbiota pre-, peri-, and postnatally and, furthermore, seeks to clarify the suggested potential factors influencing the gut microbiota in pregnancy and in the first period of life.