MR1 (MHC-related protein 1) is an antigen-presenting molecule that presents small molecule ligands to mucosal-associated invariant T cells (MAIT cells). MR1 associates with β2-microglobulin (β2M) and can bind with microbial and non-microbial metabolites, which causes the MR1 molecule to translocate from the endoplasmic reticulum to the cell surface. Here we describe the expression and two-step purification of the MR1 (K43A)/β2M stable complex in which size exclusion chromatography (SEC) was able to separate aggregated protein from the stable heterodimer complex.