Infection of BALB/c mice with murine cytomegalovirus (MCMV) decreased the numbers of cells recovered from the thymus by 80-90% after 4-7 days, although less than 10 thymocytes per million were productively infected with the virus. A loss of cortical thymocytes was evident in histologic sections and correlated with depletion of CD4+CD8+ cells.Thymic involution was minimal in C57BL/6 mice. This resistance was not H-2b-associated, as BALB.B (H-2b) mice were severely affected. In CYB recombinant inbred mice, thymic involution and MCMV replication co-segregated with atrophy and infection of the spleen and bone marrow. This suggests common regulation by natural killer (NK) 1.1+ cells, consistent with the enhanced thymic involution demonstrated in NK-deficient bg/bg mice. However, CD4-CD8- cells were not depleted, so bone marrow hypoplasia may not be the proximal cause of thymic involution.MCMV infection activated CD4+, CD8+ and CD4+CD8+ thymocytes, as expression of MEL14, major histocompatibility complex class I (H-2) and Sca-1 antigens increased on these cells. In vitro lymphoproliferation and interleukin (IL)-3 release were enhanced in unseparated and CD4+-enriched thymus preparations. Maturation of the thymus population was also evident from the high frequencies of single positive CD4+ and CD8+ cells and the decline in Sca-2 expression. However, unlike peripheral T cells, thymocytes from infected mice did not release IL-2. The results suggest that thymic involution accelerates the transit of cells through the thymus. The possibility that this impairs the elimination of autoreactive T cells within the thymus and promotes the autoimmune manifestations of MCMV disease is discussed.