The major histocompatibility complex class I chain-related gene A (MICA) in humans, located 46 kb centromeric to human leukocyte antigen (HLA)-B, is highly polymorphic. In addition to its primary role in immune surveillance, recent data highlight the importance of MICA in organ transplantation and in susceptibility to some diseases. In this study, 104 healthy, unrelated Han subjects recruited from central Inner Mongolia Autonomous Region, northern China, were investigated by sequence-based typing and fragment analysis for MICA allelic variation, MICA-HLA-B linkage disequilibrium, and HLA-A-Cw-B-MICA haplotypic diversity. Nineteen MICA alleles were observed, the most frequent of which were MICA*00801, MICA*010, MICA*00201, MICA*00901, and MICA*045, with gene frequencies of 23.08%, 18.75%, 12.02%, 12.02%, and 8.17%, respectively. The peculiarity in HLA-B-MICA haplotypic configurations was also uncovered. In particular, there was a clear-cut dichotomy between MICA*00801 and MICA*045 in their linkage to members of HLA-B*13 lineage, which was frequently represented in this population. A new MICA allele, MICA*059, was identified, which appeared to be evolutionarily linked to MICA*045. Haplotype HLA-A*30-Cw*06-B*1302-MICA*00801, previously not reported in other populations, was found with a frequency of 8.65% in this population. Our results provide new data about MICA genetic polymorphism in Chinese Han populations, which will form the basis for future studies of the potential role of MICA in allogeneic organ transplantation and disease susceptibility in related ethnic groups.