The major histocompatibility complex (MHC) class I related molecule I (MR1) molecule presents a wide array of small metabolites and drug-like antigens to unconventional mucosal-associated invariant T (MAIT) cells. Unlike the conventional MHC class I, MR1 is only oligomorphic with six alleles MR1*01-*06 recently identified that alter the mature protein. To investigate whether these allelic variants affect MR1 antigen presentation, we applied biochemical techniques to purify soluble forms of the MR1*02-MR1*05 alleles and engineered MR1-expressing cells to examine the binding of these variants to different metabolite antigens. We are able to show that polymorphisms harboured by MR1*04 and MR1*05 influence the MR1 ligand repertoire. We assessed whether this alteration of the ligand pool was due to conformational changes induced by the allelic polymorphisms by structurally characterising each of the MR1 variants using X-ray crystallography. In conjunction with mutagenesis analyses, we visualise a substitution mutation on the end of the MR1*05 F’ pocket that appears to be primarily accountable for the reduction in MR1*05 protein expression and functional activity. We proceeded to analyse how these polymorphisms may impact MR1-Ag processing within the ER by assessing the interactions between the MR1 variants and an ER chaperone protein, TAPBPR. We found that human TAPBPR moderately binds each of the MR1 variants insinuating a role for this chaperone in antigen loading onto the different MR1 alleles. Additionally, we observed that TAPBPR slightly higher affinity for unloaded MR1 proteins in comparison to liganded MR1, possibly functioning to stabilise ‘empty’ MR1 conformers. Conclusively, we have been able to structurally characterise the different MR1 alleles and can demonstrate that some of these allelic variations impact MR1 functional activity but do not affect interactions with ER chaperone protein, TAPBPR.