Investigation into the presence of human cytomegalovirus (HCMV) transforming mtrII and mtrIII sequences in peripheral blood lymphocyte (PBL) specimens of AIDS and high-risk patients was carried out by nucleic acid hybridization analyses. These probes were selected because they were viral-specific and lacked homology to normal cellular DNAs. In Southern blot hybridizations carried out under stringent conditions, we detected HCMV mtrII sequences associated with the high-molecular-weight DNAs of PBLs in 17 of 37 patients either with AIDS/Kaposi's sarcoma or at high risk for AIDS. In comparison, only 2 of 17 DNA specimens from PBLs of healthy blood donors showed hybridization to mtrII sequences. The inability to detect hybridization to the mtrIII region in most mtrII-positive specimens suggested a specific retention of mtrII sequences. Our study suggests that the retention of mtrII sequences in high molecular weight DNA may constitute a risk factor for the development/progression of AIDS. Alternatively, the retention of mtrII sequences may occur as a result of enhanced HCMV replication in patients with AIDS or at high risk for AIDS.