We explored the importance of the genetic markers microsatellite TNFa, HLA-DR3-DQ2, and DR4-DQ8 in diabetes mellitus. The studied groups comprised autoimmune type 1 (n = 63), nonautoimmune type 1 (n = 35), latent autoimmune diabetes in adults (LADA; n = 54), and nonautoimmune type 2 (n = 340) and these patients were compared to 117 healthy controls. HLA genotyping was done with polymerase chain reaction and sequence-specific oligonucleotides. TNFa microsatellites were determined with polymerase chain reaction and fragment size determination. Univariate analysis of these genetic risk factors demonstrated that homozygosity for TNFa2/2 was a significant risk factor for autoimmune type 1 diabetes (odds ratio (OR) = 5.82; 95% confidence interval (95%CI) 1.97-17.2), for autoimmune negative type 1 diabetes (OR = 4.63; 95%CI 1.32-16.2), and for LADA (OR = 3.90; 95%CI 1.21-12.5). Moreover, heterozygosity for HLA-DR3-DQ2/DR4-DQ8 was an important risk factor for autoimmune type 1 diabetes (OR = 16.4; 95%CI 3.60-75) as was DR4-DQ8/x (OR = 2.52; 95%CI 1.27-4.98). Heterozygosity for HLA-DR3-DQ2/DR4-DQ8 was a risk factor also for LADA (OR = 10.0; 95%CI 2.05-48.9). Neither HLA-DR3-DQ2 nor DR4-DQ8 were risk factors for nonautoimmune type 1 or type 2 diabetes. We concluded that heterozygosity for DR3-DQ2/DR4-DQ8 and to some extent homozygosity for TNFa2/2 were risk factors for autoimmune diabetes irrespective of the clinical classification.