Abstract: Twenty‐two human major histocompatibility complex (MHC) region microsatellite (Msat) markers were studied for diversity and linkage disequilibrium (LD) with HLA loci in hematopoietic cell transplant recipients and their HLA‐A, HLA‐B, HLA‐C, HLA‐DRB1, and HLA‐DQB1 allele‐matched unrelated donors. These Msats showed highly significant LD over much of the MHC region. The Msat diversity of five common Caucasian haplotypes (HLA‐A1‐B8‐DR3, A3‐B7‐DR15, A2‐B44‐DR4, A29‐B44‐DR7, and A2‐B7‐DR15) was examined using a new measure called ‘haplotype specific heterozygosity’ (HSH). Each of the five haplotypes had at least one Msat marker with an HSH value of zero indicating that only one Msat allele was observed for the particular HLA haplotype. In addition, the ability of Msats to predict HLA‐A‐B‐DRB1 haplotypes was studied. Over 90% prediction probability of two common haplotypes (HLA‐A1‐B8‐DR3 and HLA‐A3‐B7‐DR15) was achieved with information from three Msats (D6S265/D6S2787/D6S2894 and D6S510/D6S2810/D6S2876, respectively). We demonstrate how the HSH index can be used in the selection of informative Msats for transplantation and disease association studies. Markers with low HSH values can be used to predict specific HLA haplotypes or multilocus genotypes to supplement the screening of HLA‐matched donors for transplantation. Markers with high HSH values will be most informative in studies investigating MHC region disease‐susceptibility genes where HLA haplotypic effects are known to exist.