In this study, we investigated the five polymorphic Alu loci located within human major histocompatibility complex (MHC) class I region in 445 individuals from four distinct Chinese populations: Hunan Han, Inner Mongolia Han, Inner Mongolia Mongol and Guangdong Han populations, with an emphasis on the linkage disequilibrium (LD) between Alu insertions and human leukocyte antigen (HLA)-A, Cw and B loci in a southern (Hunan Province) and a northern (Inner Mongolia Autonomous Region) Chinese Han population. Our data showed that (a) the allele and haplotype frequencies of Alu and HLA-A loci did not differ significantly between the two southern Chinese Han populations and showed remarkable homogeneity in the two northern Chinese populations; (b) AluyHG had the highest insertion rate and HLA-A*02 harboring the single AluyHG insertion was most frequent among Alu insertion-bearing haplotypes in all four populations; (c) haplotypes AluyHF insertion–HLA-A*26, AluyHG insertion–HLA-A*02 and AluyHJ insertion–HLA-A*24 were in significant LD across the four groups and (d) haplotype AluyMICB insertion–HLA-Cw*06 was in significant LD in both populations, while significant LD of haplotypes AluyMICB insertion–HLA-B*54 and AluyMICB insertion–HLA-B*48 was only observed in the Hunan Han population and the Inner Mongolia Han population, respectively. Haplotype HLA-B*48-MICA gene deletion–AluyMICB insertion was observed at a frequency of about 3.85% in the latter population. Our data, together with previous reports on several Asian-Oceanian populations suggest the identity by descent of several common HLA-A allelic lineages in these modern human populations. The novel population-specific LD patterns uncovered in this study also shed new insight into HLA evolution and haplotype origin.