Extensive data have been obtained on sequence changes in the V3 region of the HIV-1 envelope protein that are associated with in vitro biological properties such as cell tropism and syncytium-inducing capacity. However, so far this concerned viruses isolated from peripheral blood mononuclear cells and thus did not discriminate between variants present in T lymphocytes or in monocytes. In this study, we analyzed viral sequences derived separately from uncultured T lymphocytes, blood monocytes, and plasma of an HIV-1-infected patient showing a neurological evolution of the disease. Sequences related to the V3 region and 18 amino acids downstream were obtained from 48 clones after PCR amplification. One predominant viral sequence close to the monocytotropic/non-syncytium-inducing (NSI) consensus sequence was observed in the three blood sources. Two viral species were specifically identified in monocytes (43% of the clones), showing clear differences from the consensus sequence and exhibiting the genetic determinants associated with the SI phenotype. Plasma-derived viruses with a similar V3 loop were obtained on in vitro isolation. Analysis of the biological properties of these selected viruses confirmed their monocytotropism and the syncytium-inducing phenotype as expected by the cell type in which the sequences were observed and the charge of the V3 loop. Structural analysis of these variants suggested an intermediate structure between NSI/monocytotropic and SI/lymphotropic V3 loops. Thus, in vivo circulating monocytes could be a reservoir for distinct HIV-1 variants with potential SI characteristics, at least in later stages of infection. Studying such variants over the course of the infection may shed light on their involvement in disease manifestations.