Fragments of cloned rat class I transplantation antigen genes were used to define the polymorphism detected between two lines of closely related BB rats. One line, BB-Hagedorn (BB/H), is prone to diabetes, and the other (BB control) is resistant. A cDNA probe representing part of the second extracellular domain of a class I antigen detected several DNA fragments and revealed a 2kb fragment present in resistant, but absent in diabetes-prone, BB/H rat DNA following digestion with BamH1. A 40 by cDNA probe from the same domain showed a further simplified pattern in the DNA hybridization analysis. Only two fragments, 15 kb and 7 kb, were present in the resistant rats; the diabetes-prone BB/H rats lacked the 7 kb fragment. Several lines of evidence suggest that the gene contained in this 7 kb fragment may be deleted. Analysis of other diabetic BB rats and in the F2 generation of intercross offspring of F1 hybrid parents following cross-breeding between the resistant (BB-control) and diabetes-prone (BB/H) line demonstrate that the class I polymorphism was not linked directly to diabetes. Examination of various other BB lines and sublines indicate that these polymorphisms can be traced back to at least one other subline (Worcester) in the parent colony.