Monoclonal antibodies reacting with thyroid microsomes have been described. In this report, we present evidence that some of these monoclonal antibodies (MoAb) MAH C3 and perhaps MAH C6 are directed towards the thyroid microsomal antigen towards which microsomal autoantibodies from Hashimoto patients are directed. Immunofluorescence on cryostat sections with MAH C3 and MAH C6 on thyroid gland gave cytoplasmic staining patterns that were comparable to those obtained with autoantibodies. By western blotting, reactivity of MAH C3 was shown to be directed towards a 105,000 mol. wt component, comparable to that recognized by autoantibodies by immunoprecipitation. Double immunofluorescence with MAH C3 and autoantibodies on cultured, viable thyroid monolayers revealed a large number of comparable binding sites; in contrast, binding sites for asioloagalactothyroglobulin were different of binding of MAH C3 by the autoantibodies suggesting that the epitopes recognized were different. This was confirmed with the use of a rat thyroid cell line FRTL-5 and fluorescence activated cell sorter analysis which showed binding to the rat microsomal component with autoantibodies but negligible binding with MAH C3 and MAH C6. It therefore appears that the monoclonal antibodies recognize species specific determinants while the autoantibodies recognize species cross reactive determinants. These monoclonal antibodies will be useful for purification and immunochemical analysis of this autoantigen in human thyroid disease.