For the analysis of the genetic background of autoimmune thyroiditis we used the Obese strain (OS) chicken model which develops a SAT. Practically all animals from this strain show severe lymphoid infiltration of the thyroid gland and circulating autoantibodies against thyroglobulin (Tg-AAb) within a few weeks after hatching. Of the 3 MHC haplotypes (B5, B13, B15) present in the OS, B13 was mostly associated with severe thyroid infiltration. Haplotypes B5 and B15 were associated both with severe, as well as with mild infiltration. To clarify these controversial results published by different groups and to further assess the role of the MHC in the development of SAT, we selected by appropriate breeding sublines with high and low levels of Tg-AAb. With the help of serological methods and GvH assays we were not able to find additional differences in the MHC antigens of that line. Therefore, for further characterization of these haplotypes, RFLP analysis was applied in the present study. Southern blots were done with restriction enzyme digests of erythrocyte DNA hybridized with a chicken cDNA probe (code-p234) for MHC class II antigens. The Southern blots with BamH-I digests showed at least 5 bands, four of which were polymorphic. Four RFLP patterns emerged, two of which were observed within chickens with the B15 haplotype. The confirmation of this RFLP heterogeneity within serologically identical haplotypes requires additional analysis.