The MHC class III region contains many genes that are good candidates for involvement in autoimmune disease. We report the mapping and characterization of 10 novel (CA)n microsatellites spanning the region, which are highly informative and suitable for linkage and association studies. We used these markers to identify haplotypes of MHC class III microsatellite alleles in DNA from cell lines homozygous for MHC class II and class I alleles.