The outcome of infections with three CVB4 strains known to replicate in human pancreatic islet cells (E2, V89 4557 and VD2921) and one CVB3 strain (Nancy) in CBA/J mice with regard to viral replication, inflammation and glucose tolerance was studied. Isolation of virus from hearts, livers and pancreata was performed 7, 14 and 21 days post infection (pi). All strains could be equally well isolated from the pancreata and all but one strain, V89 4557, could be isolated from the hearts. The titers of neutralizing antibodies in the mice infected with the CVB4 strain V89 4557 were significantly lower than in mice infected with the other strains (p < 0.01). Even though virus was isolated from both heart and pancreata, immunohistochemical staining only revealed inflammatory cells in the latter. Seven days pi there was a significant difference between the strains in this respect i.e. mice infected with CVB3 and the E2 strain revealed more CD4+ lymphocytes, macrophages and granulocytes compared to mice infected with the other CBV strains (p < 0.05). Glucose tolerance tests performed at day 14 and at day 115 pi revealed normal kinetics of glucose absorption from the blood in the control mice and in mice infected with the strains that induced severe inflammation of the pancreas (E2 and CVB3). In contrast, the glucose clearance in mice infected with the CVB4 strains V89 4557 and VD2921 were significantly impaired compared to uninfected controls and compared to mice infected with the other CVB strains (p < 0.01). Mice infected with CVB4 strains V89 4557 also had a significantly impaired clearance of glucose 120 min after injection (p < 0.05) even though no virus could be isolated and no inflammation was detected in the pancreata at that time point. These results show that there is a clear strain difference with regard to the ability to affect clearance of glucose from the blood as late as 115 days pi as well as the degree of inflammation in the pancreas. This indicates that the in vitro diabetogenic strains (VD2921 and V89 4557) also in vivo can induce a pre-diabetic state in CBA/J mice.