We detected insulin2 mRNA but not insulin1 in thymus using real-time PCR analysis. Transgenic expression of a mutated insulin message (alanine rather than tyrosine at insulin B chain amino acid 16) was variably induced in thymus of four transgenic founder strains. The transgenic message levels were as high or higher than native insulin2 message. Lack of the insulin2 gene resulted in the enhancement of anti-insulin autoantibodies (regular NOD vs insulin2-knockout NOD, P<0.001) and in the presence of the B16:A insulin transgenes, levels of insulin autoantibodies remained elevated (regular NOD vs insulin2-knockout NOD with B16:A insulin, P<0.01). Diabetes acceleration by the knockout of the insulin2 gene was not influenced by the presence of the B16:A insulin transgenes. These data suggest that the B16:A insulin does not compensate for lack of native insulin expression in thymus. If lack of thymic insulin message of the insulin2 knockout is the cause of diabetes acceleration, this suggests that native insulin B:9-23 sequences may be crucial in thymus for insulin mediated immunomodulation. Further experiments varying native insulin message expression in thymus is necessary for direct comparison, but the current study provides additional evidence of the potential important role of a specific insulin B chain epitope.