To evaluate potential differential diabetes risk of DR3 haplotypes we have evaluated class I alleles as well as two microsatellites previously associated with differential risk associated with DR3 haplotypes. We found that over one-third of patient DR3 chromosomes consisted of an extended DR3 haplotype, from DQ2 to D6S2223 (DQ2, DR3, D6S273-143, MIC-A5.1, HLA-B8, HLA-Cw7, HLA-A1, and D6S2223-177) with an identical extended haplotype in controls. The extended haplotype was present more frequently (35.1% of autoimmune-associated DR3 haplotypes, 39.4% of control DR3 haplotypes) than other haplotypes (no other haplotype >5% of DR3 haplotypes) and remarkably conserved, but it was not transmitted from parents to affected children more frequently than nonconserved DR3-bearing haplotypes. This suggests that if all alleles are truly identical for the major A1, B8, DR3 haplotype (between A1 and DR3), with different alleles on nonconserved haplotypes without differential diabetes risk, then in this region of the genome DR3-DQ2 may be the primary polymorphisms of common haplotypes contributing to diabetes risk. Diabetes 54: 1879 -1883, 2005 A number of studies are now evaluating the development of anti-islet autoantibodies in both children from the general population and first-degree relatives of patients with type 1 diabetes (1-3). It is clear from these studies that anti-islet autoantibodies can develop either in the 1st year of life or, subsequently, that anti-insulin autoantibodies are frequently the first autoantibody expressed, and that the presence of multiple anti-islet autoantibodies and persistent autoantibodies are associated with a high risk of progression to type 1 diabetes in both the general population and in relatives. Many of the current studies have evaluated risk based upon HLA class II alleles (4 -7). The highest-risk genotype for early-onset type 1 diabetes and expression of anti-islet autoantibodies consists of DR3-DQ2 (DQA1*0501-DQB1*0201) on one chromosome and DR4-DQ8 (DQA1*0301-DQB1*0302) on the second chromosome (7). Most studies currently evaluate children for the expression of autoantibodies reacting with GAD65, insulinoma-associated protein 2 (ICA512), and insulin autoantibodies. The risk for children with the DR3-DQ2/DR4-DQ8 genotype in general population is Ͻ5% for the development of persistent anti-islet autoimmunity by age 5 years versus Ͼ20% for offspring and perhaps as high as 40% for siblings (of a patient with type 1 diabetes) with the same DR/DQ genotype (8). Such a remarkably high risk for anti-islet autoimmunity among relatives with DR3/DR4 suggests that other alleles within the major histocompatibility complex (MHC) may be contributing risk, in addition to the class II alleles, in that most often siblings of probands with diabetes who are DR3/DR4 are HLA identical to the proband (two identical haplotypes). It is also likely that non-MHC alleles contribute to this increased risk, but by specifying HLA genotype, only this chromosomal region is "fixed" to usually be identical to the ...