The prevalence rate for autoimmune thyroid disease (ATD) is about 30 times higher in the type I diabetic (IDDM) families that were ascertained for Genetic Analysis Workshop 5 (GAW5) than in the general population. Two approaches were used to study the clustering of ATD and IDDM in these families: (1) HLA haplotype sharing in sib pairs in which one has IDDM and other has ATD was analyzed with the genetic interrelationship method. The hypotheses of different alleles (at the same locus or at different loci) were rejected. Thus there must exist at least one common allele that predisposes to both IDDM and ATD. (2) The DR genotype frequencies suggest that in the GAW5 families two alleles may be predisposing to ATD; a recessive DR3-associated allele and a dominant DR4-associated allele.