The Qa-6 alloantigen and the molecule that crossreacts with the monoclonal antibody (mAb) 20-8-4 have been shown to be serologically distinct from the Qa-2 alloantigen by strain distribution and tissue distribution, respectively. In this report, we address the biochemical relationships among Qa-2, Qa-6, and the 20-8-4 cross-reactive molecule by using immunoprecipitation and polyacrylamide gel electrophoresis. Each of these molecules had an apparent m.w. of approximately 41K and was associated on the cell surface with beta 2-microglobulin. Removal of N-linked oligosaccharides with endoglycosidase F reduced their apparent m.w. to approximately 33K to 34K. The determinants recognized by anti-Qa-6 and mAb 20-8-4 were shown to reside on the same molecule(s) precipitated by anti-Qa-2 sera by immunodepletion experiments. The mAb 20-8-4 was also shown to preclear the molecules detected by the Qa-6 and Qa-2 antisera. Two-dimensional gel electrophoresis analysis demonstrated complete co-migration of the approximately 41K molecules detected by the three antibodies. By peptide map analysis with V8 protease, all three molecules appeared identical. Also, the determinant recognized by Qa-6 antiserum co-modulated with that recognized by the anti-Qa-2 mAb D3.262. Taken together, these results demonstrate that the molecules recognized by these three antisera and/or mAb are biochemically indistinguishable. These data, in conjunction with the serologic and genetic findings suggest that mAb 20-8-4 recognizes a molecule that is biochemically similar and possibly identical to the Qa-2 antigen. Moreover, although the genetic, serologic, and biochemical data demonstrate that Qa-6 is not controlled by the Qa-2 locus, but rather by a gene telomeric to Qa-2, the molecule bearing the Qa-6 determinant is very similar, if not identical, to the Qa-2 molecule. Several possible explanations for these discrepancies are discussed.