The study of genetic markers linked and associated with disease has provided important evidence of a genetic contribution to numerous diseases and has helped to establish their modes of inheritance. However, this information has not been fully utilized in counseling individuals at risk for these disorders. In the case of recessive, marker-linked diseases, such as idiopathic hemochromatosis linked to HLA in family studies and associated with specific HLA alleles in population surveys, the only current clinical application has been to identify siblings who share both HLA-marker haplotypes with the affected proband. They are considered to be presymptomatically affected, and more definitive invasive investigations are considered appropriate. All other relatives, including parents, offspring and other siblings, who share only 1 marker with the proband, have been counseled only that their risk is equivalent to the gene frequency of the disease allele, e.g., 3-6% for hemochromatosis. A generally applicable method was developed here to utilize population association data to derive more specific and accurate risk figures for these other relatives of patients with marker-linked and associated diseases. This method was applied to idiopathic hemochromatosis. If the offspring of a patient with hemochromatosis lacks A3, B7 and B14, the risk to that offspring for developing hemochromatosis is less than 2%. On the other hand, if they receive HLA A3 from their unaffected parent, their risk climbs to 9-10%; if they receive an A3-B14 haplotype, their risk increases to virtually 100%. The application of association data to family members already at a basal increased risk for marker-linked disease can significantly refine the disease risk estimates given to those relatives. This information can be utilized to select individuals in whom invasive diagnostic testing or preventative intervention is indicated.