Fourteen patients suffering from haemophilia B have been screened for deletions and mutations. None of them produce antibodies against native factor IX. Three patients from the same family were found to have a total deletion of the factor IX gene. Two of the patients, who are cousins, have inherited the same maternal HLA haplotype indicating that postulated immune gene(s) located at the MHC locus might be of importance for the development of antibodies against factor IX. DXS99 is a locus closely linked to the factor IX gene and a recombination event in this family makes it likely that this locus is centromeric to the factor IX gene.