Polymorphisms of CCR5, CCR2, SDF, and CX3CR1 were reported to be involved in HIV-1 infection or the development of disease progression to AIDS. Cohort studies showed that CCR5-Delta32, SDF1-3'A, and CCR2-64I were protective, which could provide resistance to HIV-1 infection or delay disease progression, although the effect of SDF1-3'A homozygosity in the later stage of progression to AIDS was still controversial. The two SNPs of CX3CR1-249I and 280M were independent risk factors, which could accelerate the progression to AIDS. In this study, we surveyed the frequency distributions of the five alleles in Chinese populations using PCR and PCR-RFLP. We found that the frequencies of the alleles varied substantially from population to population. We also observed that there was a large discrepancy between these alleles among populations of the north and south. Populations in the same language-speaking family or with the same origin shared similar allele distributions. Furthermore, genotype distributions were found to be in accordance with Hardy-Weinberg equilibrium and a significant linkage disequilibrium was observed between 249I and 280M. The comprehensive genotype analysis of the three-locus CCR5-Delta32, CCR2-64I, SDF1-3'A, and CX3CR1-249I-280M haplotypes for the first time provides host genetic information for future studies of HIV infection and disease progression in Chinese populations.