The inbred BALB/c mouse has three transplantation antigens, H2-Kd, H2-Ld, and H2-Dd. We present the complete nucleotide sequence of the H2-Dd gene as well as 777 residues of previously unpublished H-2Dd protein sequence. These data complete the sequences of all the BALB/c transplantation antigen genes and permit detailed comparison with each other and with their counterparts from the inbred C57BL/10 mouse. Transplantation antigens may differ from one another by as much as 5%-15% of their amino acid sequence for the external domains. These extensive differences may arise by gene conversion. The H-2D region of the BALB/c mouse encodes the H2-Dd and the H2-Ld genes. Serologic data suggest that at least two additional transplantation antigen molecules, H2-Rd and H2-Md, are encoded in the H-2D region of the major compatibility complex. Paradoxically, gene cloning studies have only identified the H2-Dd and the H2-Ld genes in the H-2D region. A complete DNA sequence of the H2-Dd gene shows that a variety of alternative splice sites exist throughout the gene, which may lead to additional gene products and may explain the multiplicity of H-2D-encoded polypeptides.