Stromal-derived factor (SDF-1) is the principal ligand for CXCR4, a co-receptor with CD4 for T lymphocyte cell line-tropic human immunodeficiency virus-type 1 (HIV-1). A common polymorphism, SDF1-3' A, was identified in an evolutionary conserved segment of the 3' untranslated region of the SDF-1 gene. Sequence analysis revealed a common variant at position 801, a G-->A transition referred to as SDF1-3' A. Because this variant eliminates the Msp I restriction site PCR-restriction fragment length polymorphism (RFLP) analysis was used for rapid detection of genotypes. We genotyped 62 HIV infected patients and 60 non-HIV blood donors by RFLP analysis. We also assessed syncytia formation through co-culture of MT-2 cells with peripheral blood mononuclear cells from HIV patients. Syncytium-inducing HIV-1 variants have been shown to be clinically significant in the pathogenesis of HIV-1 infection. In our study, we detected a low frequency of 3'A/3'A (5%) in the blood donors but this genotype was absent in all HIV patients. We found that 41 (68%) HIV patients including syncytia inducing (SI) and non-syncytia inducing (NSI) groups contained the wild type (wt/wt) genotype for SDF-1. Our data indicate that there is no correlation between SDF-1 alleles and syncytium inducing HIV.