Mta, the maternally transmitted antigen of mice, is a hydrophobic, N-formylated mitochondrial peptide, MTF, presented on the cell surface to cytotoxic T lymphocytes by a novel major histocompatibility complex class I molecule, encoded by H-2M3. We have cloned and sequenced two alleles of M3, which differ in their ability to present MTF despite greater than 99% identity in the coding regions. M3 is as divergent from classical, antigen-presenting H-2 molecules as from other class I genes of the Hmt and the Qa/Tla regions. Amino acids critical for folding of class I molecules are conserved in M3. Noncharged amino acids lining the peptide-binding groove and phenylalanine 171 may explain the unique interaction with MTF, and leucine 95 appears critical for immunological activity.