Coxsackievirus B (CVB) most commonly causes a self-limited febrile illness in infants, but in severe cases can manifest in acute systemic inflammatory diseases including meningo-encephalitis, pancreatitis, and myocarditis. Chronic consequences of mild CVB infection are unknown, though there is an epidemiologic association between early subclinical infections and late heart failure, raising the possibility of subtle damage leading to late-onset dysfunction, or chronic ongoing injury. Huang and colleagues described a mouse model where neonatal exposure to doxorubicin depleted cardiac stem cells (CSCs) and resulted in cardiac dysfunction in adult animals that was only elicited by a prolonged exercise challenge or surgical myocardial infarction. Additionally, Feuer et al have shown that CVB infects and destroys actively proliferating neural stem cells. Here we report that cultured CSCs from neonatal mouse hearts were also susceptible to CVB infection. To test the hypothesis that CVB might deplete CSCs during self-limited infection, we inoculated neonatal mice with CVB and assessed the effects of viral infection on CSCs. We observed infected CSCs in the neonatal heart as well as a 50% reduction in CSCs in adult animals previously exposed to CVB. Our observations indicate that CVB can target and infect CSCs in the neonatal heart, subsequently exhausting them. Shortly after infection, we observed the induction of premature differentiation in the surviving CSCs which contributed to the sustained depletion of CSCs in adults. When these animals were physiologically stressed as adults via exercise of pharmacological stimulation, they exhibited cardiac hypertrophy and fibrosis. This supports the hypothesis that predisposition to heart failure can be a sequel to asymptomatic CVB infection. We hypothesize that asymptomatic CVB infection may result in sensitivity to cardiac injury and that this is due to depleted CSCs. Additionally, because CVB is known to upregulate host autophagy after infection, we explored how autophagy might be involved in CSC depletion and viral dissemination. We found that CVB induced the release of extracellular microvesicles that contained large amounts of virus. Because viral particles would be sequestered within host-derived membranes, we hypothesize that these vesicles may be a novel mode of host cell escape that bypasses humoral immune defenses.