The genetic basis of idiopathic hemochromatosis, a common disorder of iron metabolism, has remained an enigma for over two decades. In an attempt to refine the chromosomal localization of this gene, we have conducted a linkage disequilibrium mapping study utilizing a large group of unrelated American patients. The 12 microsatellites used as genetic markers in this analysis include a series of recently described polymorphic dinucleotide (D6S1558, D6S1545 and D6S1554) and tetranucleotide (D6S1016 and D6S1281) repeats which map between D6S105 and D6S299. Haplotype reconstructions indicate that a core genotype, composed of D6S464 allele 3/D6S1260 allele 4/D6S1558 allele 5, exists on a majority of disease chromosomes. Stringent statistical measures of marker-disease disequilibrium suggest that only associations with D6S1260 are significant and furthermore, aid in the assignment of refined centromeric and telomeric limits for the likely location of the hemochromatosis gene. In summary, the genetic data presented in this report predict that the hemochromatosis locus resides between D6S464 and D6S1558, most likely very close to marker D6S1260. Because a single yeast artificial chromosome clone contains all three of the above loci, a thorough search for coding sequences in this region is likely to identify the gene mutated in this common disorder.