The optimal healthy microbiota during early life still needs further evaluation. Pre- and probiotics are commonly used as supplementation in infant formula.Prebiotic oligosaccharides stimulate the growth of bifidobacteria aiming to mimic the gastrointestinal microbiota of breastfed infants. In general, results with prebiotics in therapeutic indications are disappointing.Studies suggest that probiotic supplementation may be beneficial in prevention and management of disease such as e.g., reducing the risk of necrotizing enterocolitis in preterm infants, prevention and treatment of acute gastroenteritis in infants, etc. Although many studies show promising beneficial effects, the long-term health benefits and eventual risks of probiotic supplementation during early life are not clear.It is likely that ongoing research will result in the use of specific probiotic organisms and/or prebiotic oligosaccharides during the first 1,000 days of life, with the goal to develop a healthy microbiota from conception over birth into the first two years of life with a lowered risk of infections and inflammatory events.