The CD1 locus encodes a family of major histocompatibility complex (MHC) antigen-like glycoproteins which associate with beta 2-microglobulin and are expressed on immature thymocytes and Langerhans cells. Three CD1 molecules have been identified by monoclonal antibodies and molecular cloning: CD1a, -b, and -c. We have isolated a cDNA coding for a fourth CD1 molecule from a human thymocyte library and termed this molecule CD1d. Reported here are the complete nucleotide sequence and genomic organization of CD1d. They predict that this molecule is related to the previously identified CD1a, -b, and -c molecules and to MHC class I molecules, with three external domains, a transmembrane domain, and a short cytoplasmic tail. The sequence of CD1d is the most divergent among the CD1 molecules in the membrane-distal alpha 1 and alpha 2 domains and in the 5' untranslated region. In contrast, all four CD1 molecules are highly homologous in the membrane-proximal alpha 3 domain, which is likely involved in beta 2-microglobulin binding. A comparison of CD1 and MHC class I sequences suggests that these molecules each evolved to interact with a distinct set of cell surface proteins.