Mouse hepatitis virus (MHV) is a pervasive pathogen in most mouse colonies worldwide. Infection with this virus, which is often inadvertent and unrecognized, has previously been correlated in numerous anecdotal reports with immune modulation seriously affecting the outcome of biomedical experiments. Studies using experimental models to examine the effects of MHV infection have demonstrated that the virus can both stimulate and depress immune function in vitro. We have used intranasal infection of MHV-susceptible BALB/c mice with MHV strain A59 to examine the effects of this virus on lymphoid tissue composition as well as immune function both in vitro and in vivo. We observed that the thymus, spleen, and lymph nodes underwent a transient period of marked cellular depletion. During that time, the percentages of T and B cells in the spleen remained normal. However, within 1 week after inoculation, splenic lymphoid cell proliferation was significantly decreased in response to the T-cell stimuli, concanavalin A and anti-CD3 monoclonal antibody. This continued through day 35 but was resolved by 102 days postinoculation. Notably, at days 35 and 102, mice infected with MHV-A59 were unable to reject skin grafts at a rate comparable to normal animals. These results support a basis for in vitro and, importantly, long-term in vivo immune dysfunction after infection with MHV.