We have previously described an Mls-1a-like clonal deletion of mature CD4+ T cells which express V beta 6 and V beta 8.1 chains of the TCR in half of the mice of a BALB/c, Mls-1b colony (BALB/c IC). This occurs in the absence of the Mtv-7 provirus which is responsible for the clonal deletion in Mls-1a mice. We developed a polymerase chain reaction assay in order to study the presence of retroviral transcripts homologous to the viral superantigen gene (vSAG) of Mtv-7 and Mtv-6 in various tissues. Mtv-7 homologous transcripts were present in the mammary glands of lactating BALB/c IC mice and in the thymuses and/or spleens of BALB/c IC virgin mice with deletion of V beta 6+ lymph node T cells, and not in BALB/c IC with normal V beta 6 expression. These results indicate that this BALB/c colony is infected with an exogenous mouse mammary tumour virus (MMTV) whose vSAG is similar to Mtv-7, as recently reported. Thymectomies performed at 4-5 weeks of age (at least 4 weeks before detection of clonal deletion), did not affect the occurrence of clonal deletion in peripheral lymph nodes when tested 20 weeks later. This suggests that clonal deletion can be achieved without further intrathymic contact with the antigen. Since MMTV is transmitted through milk and is likely to be present in the gut, we evaluated the percentage of V beta 6+CD4+ T cells within the gut intraepithelial lymphocyte (IEL) population. Mice with normal V beta 6 expression in lymph nodes may show partial deletion of V beta 6+CD4+ IEL.(ABSTRACT TRUNCATED AT 250 WORDS)