Abstract Wasted mice bear an autosomal recessive mutation (wst) that causes neurologic abnormalities, faulty DNA repair in lymphocytes, and immunodeficiency at mucosal sites. Recent work has suggested possible viral involvement in these manifestations by demonstrating abnormal viral gp70 expression that segregates with the wasted mutation. In the experiments reported here, we examined tissue-specific expression of AKR viral (AKV) sequences and virus-like 30S (VL30) elements in wasted and control mice. Our studies showed that AKV and VL30 RNA expression were two- to fivefold higher in spleen, brain, and thymus of mice bearing the wst allele than in those of control mice. (These tissues have all been shown to display functional or developmental abnormalities in wst/wst mice.) Expression of viral mRNA in Peyer's patches and mesenteric lymph nodes was similar in wasted and control animals. The majority of the VL30-hybridizing RNA in all tissues could be attributed to long-terminal-repeat rather than to main-body sequences. These differences in expression between wasted and control mice could not be attributed to differences in VL30 or AKV gene copy number. Our results demonstrate an association between altered expression of viral and virus-like sequences and the development of tissue-restricted abnormalities in wst/wst mice.