We have investigated mechanisms involved in immunodominance of the CTL response of C57BL/6 (B6) mice against cells of BALB.B origin. This transplantation barrier consists of at least 40 minor histocompatibility (H) Ags. Insufficient presentation of nondominant epitopes in the presence of dominant epitopes was investigated as a possible mechanism for immunodominance. Ag presentation was assessed by recognition of dendritic cells of BALB.B origin, MLC restimulatory capacity, and quantification of cell surface presentation by peptide elution from intact cells. Cells from BALB.B mice, which fail to elicit CTL against nondominant epitopes, presented nondominant epitopes to a similar extent as cells from minor H congenic mice; the latter do elicit CTL against nondominant minor H Ags. Nevertheless, presentation of nondominant and dominant epitopes by the same APC appeared to be an important factor for immunodominance to occur, since simultaneous immunization with the epitopes on separate cells elicited CTL against both types of epitopes. This suggested that immunodominance is determined in the interaction between different responding T cells and the APC. Support for this was obtained in an in vitro model in which the CTL response against a nondominant epitope was inhibited by the concomitant response against a dominant epitope. This study suggests that immunodominance in the CTL response against certain minor H Ags results from interference between T cell responses and not from insufficient presentation of peptide epitopes. The study also provides an in vitro model for further investigations of the immunodominance phenomenon.