In order to investigate the implication of viral replication in acute, subacute, and chronic infections of coxsackievirus B3 (CVB3), we examined the histopathological changes and plus- and minus-strand viral RNA dynamics in heart, pancreas, brain, and liver of CVB3-infected All mice. Mice were inoculated intraperitoneally with CVB3 and sacrificed on 1, 2, 3, 4, 7, 10, 14, 21, 30, 60, and 90 days post infection (p.i.). Plus- and minus-strand viral RNAs in the organs were quantitated and the organs were additionally evaluated histopathologically for inflammation. No inflammatory infiltrates were observed in the liver, brain, and heart. In contrast, massive lymphocyte infiltration and fat replacement were shown in the pancreas with loss of acinar cells. Both plus- and minus-strand viral RNA levels were detected by 21 days p.i. in heart, 90 days p.i. in pancreas, 4 days p.i. in liver, and 10 days pi in brain. The plus-strand RNA was found at least fifty fold higher than the minus-strand RNA by 4 days p.i. in heart and pancreas and by 3 days pi in liver. The plus- to minus-strand RNA ratio in brain was found less than 1:20. Our data indicate that viral replication was actively occurred in heart, pancreas, and liver during acute CVB3 infection, whereas viral replication was limited in brain. Furthermore, chronic persistent viral RNA was observed in pancreas. In conclusion, CVB3 at low dose of virus induces severe pancreatitis but marginal or no inflammatory changes in the heart, liver, and brain.