Previous studies have found that intraepithelial lymphocytes (IEL) contain virus-specific cytotoxic T lymphocytes (CTL) that increase dramatically during the course of virus infection. In the present study, the T-cell receptor (TCR) V beta pattern used by IEL against reovirus enteric infection was investigated both in conventional and in germfree mice. IEL were isolated by a modified rapid method, and their expression of 13 TCR V betas was examined by flow cytometric analysis. The virus-specific CTL activity of each TCR V beta subset was assessed by subtraction with coated Dyna beads by a nonradioactive assay. There was a preferential perturbation of TCR V betas following virus challenge, including increases in cells expressing V beta7, -12, -14, and -17 in conventional mice and V beta2, -12, and -17 in germfree mice. In conventionally reared mice, IEL maintained and restimulated in culture had a preferential use of TCR V beta9, -12, and -17. TCR V beta2 and -17 subfamilies were found amplified in all conditions. Furthermore, TCR V beta12 and -17 accounted for 37 and 77% of the virus-specific CTL activity, respectively, after in vitro restimulation. This study provides evidence that virus-specific CTL activity may be due to the oligoclonal expansion of TCR V beta subfamilies in IEL. Our findings suggest that in vivo infection selectively presents few T-cell epitopes and that the correct identification of these T-cell epitopes would increase the likelihood of success when designing subunit vaccines.