Growing evidence suggests that transcriptional regulators and secreted RNA molecules encapsulated within membrane vesicles modify the phenotype of target cells. Membrane vesicles, actively released by cells, represent a mechanism of intercellular communication that is conserved evolutionarily and involves the transfer of molecules able to induce epigenetic changes in recipient cells. Extracellular vesicles, which include exosomes and microvesicles, carry proteins, bioactive lipids, and nucleic acids, which are protected from enzyme degradation. These vesicles can transfer signals capable of altering cell function and/or reprogramming targeted cells. In the present review we focus on the extracellular vesicle-induced epigenetic changes in recipient cells that may lead to phenotypic and functional modifications. The relevance of these phenomena in stem cell biology and tissue repair is discussed.