Point mutations in the reverse transcriptase (RT) gene of human immunodeficiency virus type-1 (HIV-1) have been associated with reduced sensitivity of the virus to inhibition by the antiretroviral drug zidovudine (ZDV). During therapy we have previously observed the accumulation of these mutations, at codons 41, 67, 70, 215, and 219 of the RT gene, in proviral DNA sequences from infected peripheral blood mononuclear cells (PBMCs) and in cell-free virus RNA. Using a quantitative point mutation assay (PMA) we have been able to quantify the proportions of mutant and wild-type sequences at these points in mixed populations of viral RNA and DNA derived from clinical samples. Thus we have confirmed that the mutations can be detected earlier in cell-free virus RNA than in PBMC proviral DNA and their accumulation in RNA precedes that in DNA. We have analyzed serial samples from 10 subjects undergoing zidovudine therapy and shown significantly higher levels of mutations in cell-free viral RNA than in PBMC proviral DNA at codons 41, 70, and 215 during the in vivo acquisition of the mutations. In the group of subjects studied the mean time delay between RNA and DNA reaching a given level of mutation was 25 days.