The RNA genome of the human immunodeficiency virus type 1 (HIV-1) is established as proviral DNA in infected cells. Only some of these cells may actively produce the array of viral RNAs that support progeny virion production. In vivo expression of a subset of proviral genotypes could influence the experimental characterization of the viral quasispecies. We have explored the relationship between DNA and cDNA genotypes of the envelope gene by the molecular cloning and nucleotide sequencing of these templates from noncultivated peripheral blood mononuclear cells from an HIV-1-infected patient. Eleven proviral DNA and nine cDNA clones representing the V1-V3 region of gp120 were recovered and sequenced. The proviral group was more heterogeneous than the cDNA group by nucleotide sequence changes and V1 length polymorphisms. Deduced amino acid sequences from this data set showed that the two groups were distinct in primary structure, in the position of N-linked glycosylation sites, and in the net charge of the V3 loop. The V1-V2 region discriminated between the groups more strongly than the V3 region. The differential representation of HIV-1 envelope genotypes in the cDNA versus the proviral compartment may have important implications for the pathogenesis of disease and for the design of antiviral therapeutics.