CD1 and MR1 are major histocompatibility complex (MHC) class I-related proteins that bind and present non-peptide antigens to subsets of T cells with specialized functions. CD1 proteins typically present lipid antigens to CD1-restricted T cells, whereas MR1 presents vitamin B-based ligands and a variety of drugs and drug-like molecules to MR1-restricted T cells. The CD1 family of antigen presenting molecules has been divided into two groups: Group 1 contains CD1a, CD1b and CD1c, and Group 2 contains CD1d. Additionally, CD1e is expressed intracellularly and is involved in the loading of lipid antigens onto Group 1 CD1 proteins. Humans express both Groups 1 and 2 CD1 proteins, whereas mice only express CD1d. Group 1 CD1 proteins present lipid antigens to T cells that generally express diverse T cell receptors (TCRs) and exhibit adaptive-like functions, whereas CD1d presents lipid antigens to subsets of T cells that express either diverse or highly restricted TCRs and exhibit innate-like functions. CD1d-restricted T cells are called natural killer T (NKT) cells, which includes Type I or invariant NKT (iNKT) cells expressing semi-invariant TCRs, and Type II NKT cells expressing more diverse TCRs. CD1-restricted T cells have been implicated in a wide variety of diseases, including cancer, infections, and autoimmune, inflammatory and metabolic diseases. Additionally, NKT cells have been targeted for immunotherapy of disease with ligands such as α-galactosylceramide for iNKT cells, or sulfatide for Type II NKT cells. Like iNKT cells, MR1-restricted T cells express semi-invariant TCRs and display innate-like functions. MR1-restricted T cells, also called mucosal-associated invariant T (MAIT) cells, have been implicated in immune responses against a variety of pathogens such as Mycobacterium tuberculosis, Pseudomonas aeruginosa, Helicobacter pylori, hepatitis C virus and influenza virus. Moreover, these cells contribute to autoimmune and inflammatory diseases, including colitis, rheumatoid arthritis, psoriasis, lupus, and diabetes.