The composition of the gut microbiota, and thus also the modification of the gut microbiota by specific probiotics or prebiotics early in life, may have an impact on the risk of disease in the child. Above the impact on gut microecology, probiotic effects have been attributed to restoration to normal of increased intestinal permeability, improvement of the intestine's immunological barrier functions, alleviation of the intestinal inflammatory response, and reduced generation of proinflammatory cytokines characteristic of local and systemic allergic inflammation. Recent demonstrations from experimental and clinical studies suggest that the gut microbiota is also involved in the control of body weight and energy metabolism, affecting the two main causes of obesity: energy acquisition and storage, and contributing to insulin resistance and the inflammatory state characterising obesity. Current research focuses both on characterising specific probiotic strains and on how the food matrix and the dietary content interacts with the most efficient probiotic strains. It is important to characterise each probiotic to species and strain level and to select strains with documented properties, the probiotic potential being strain-specific. As any proof of causality requires clinical intervention studies in humans in different populations, rigorous and detailed documentation will enhance reproducibility and circumvent confusion.