The non-obese diabetic (NOD) mouse is a polygenic model of insulin-dependent diabetes. To better understand the biology, immunology and genetics of this mouse strain NOD mice were typed for RFLP at 29 loci and microsatellite variation at a further nine loci. Mice were also typed for the expression of lymphocyte differentiation antigens. Comparisons were made with two non-diabetic strains, C57BL/6 and SJL, for these markers. A number of restriction fragment length polymorphisms (RFLP) were defined: seven between C57BL/6 and NOD; five between SJL and NOD; and four in which both C57BL/6 and SJL differed from NOD. Previously reported microsatellite results were extended by defining the SJL alleles at these loci, finding five loci at which NOD differed from B6 alone, and four loci at which NOD differed from both B6 and SJL. In addition, the NOD Igh allotype and alleles for a number of lymphocyte differentiation antigens were defined for the first time. The expression of uncommon alleles of these antigens suggests candidates whose role in the diabetogenic process can be tested.