Summary.The non-obese diabetic (NOD) mouse strain which spontaneously develops diabetes is a model for human Type 1 (insulin-dependent) diabetes mellitus. At least one of several genes controlling diabetes in the NOD mouse has been mapped to the MHC. Although previous experiments have implicated the MHC class II genes in the development of the disease, the existence of other MHC linked susceptibility genes has not been ruled out. In order to identify these susceptibility genes we have further characterized the MHC haplotype of the NOD mouse and two non-diabetic sister strains, the non-obese non-diabetic (NON) and cataract Shionogi (CTS). We have examined the mouse MHC class III region for the presence of homologous genes to 17 newly isolated human MHC class III region genes (G1, G2, G4, G6, G7a/valyl-tRNA synthetase, HSP70, G8, G9, G10, G12, G13, G14, G15, G16, G17 and G18). We detect unique hybridizing DNA fragments for 16 of the 17 genes in six inbred mouse strains (NOD, NON, CTS, B10, BALB/c and CBA/J) indicating that this part of the H-2 region is similar to the human MHC class III region. Using a panel of restriction enzymes we have defined RFLPs for 6 (G2, G6, HSP70, G12, G16, G18) of the 16 cross-hybridizing probes. The RFLPs demonstrate that NOD, NON and CTS mouse strains each have a distinct MHC haplotype in the MHC class III region.Key words: MHC class III region, non-obese diabetic mouse, non-obese non-diabetic mouse, cataract Shionogi mouse, Type 1 (insulin-dependent) diabetes mellitus, restriction fragment length polymorphisms.The non-obese diabetic (NOD) mouse which spontaneously develops diabetes, is an animal model for Type 1 (insulin-dependent) diabetes mellitus. As in man the disease in this mouse strain has an autoimmune aetiology. Type 1 diabetes in the NOD mouse is controlled by several recessive genes [1, 2] at least one of which, Idd-1, has been mapped to the MHC on chromosome 17. Analyses of transgenic NOD mice containing foreign or modified MHC class II genes have demonstrated that the lack of I-Ect expression [1] and the unusual sequence of the AflgT-chain [3] are critically important for the diabetic phenotype [4][5][6][7]. The NOD mouse strain was developed from a non-inbred cataract prone ICR mouse strain together with two non-diabetic strains, the non-obese non-diabetic (NON) and the cataract Shionogi (CTS) mouse strains [8]. Previous analyses have shown that the NOD and CTS mouse share the same alleles in the MHC class II region, but are different at the H-2D locus [9][10][11]. The NOD and NON mouse strains share the same functional allele for the H-2D locus [9], but differ in the rest of the classic and non-classic class I and class II loci [2, 9, 12]. Congenic NOD.CTS-H-2 strains are being established, and preliminary analysis of these suggests that in addition to the MHC class II genes at least one other MHC-linked gene might influence the diabetogenic phenotype [13].The MHC contains three major subregions. The highly polymorphic class I and class II regions encode the receptors...