Early-life development has a direct effect on the long-term health of an individual. some of the main processes influencing early-life development are epigenetic modifications, i.e., mechanisms that promote changes in gene expression in the context of the same DNA sequence, and changes in the human microbiota, i.e., living organisms located on or within humans with prime examples being the human microorganisms located in the human gastrointestinal system. These processes can be mediated by extracellular vesicles, which are essential agents of cell-to-cell communications. Exosomes, a subgroup of extracellular vesicles, are of particular interest in early life, since they have been shown to be associated with the development of infant immune response, neuronal function and metabolism. The present review summarizes the latest literature on the effects of epigenetic modifications and microbiota changes in early-life development, and discusses the mechanisms through which exosomes may mediate such changes. A special mention is also made to human breast milk, since several of the benefits associated with breast feeding could be potentially linked with the microbiota and the exosomes it contains.