The intestinal microbiota can influence host metabolism. When given early in life, agents that disrupt microbiota composition and consequently its metabolic activity, can influence body mass of the host by either promoting weight gain or stunting growth, which is consistent with effects of the microbiota on development. In this Perspective, we posit that microbiota disruptions in early-life can have long-lasting effects on body weight in adulthood. Furthermore, we examine the dichotomy between antibiotic-induced repressed or promoted growth and review the experimental and epidemiological evidence that supports these phenotypes. Considering the characteristics of the gut microbiota in early life as a distinct dimension of human growth and development, as well as comprehending its susceptibility to perturbation, will allow for increased understanding of human physiology and could lead to development of interventions to stem current epidemic diseases, such as obesity and types 1 and 2 diabetes mellitus.