Molecular polymorphism influences the strong association of HLA-B27 with ankylosing spondylitis through an unknown mechanism. Natural subtypes and site-directed mutants were used to analyze the effect of altering the peptide-binding site of this molecule on its stability, interaction with tapasin, folding, and export. The disease-associated subtypes B*2705, B*2702, and B*2704 showed higher thermostability at 50°C than all other subtypes and mutants, except some mimicking B*2702 polymorphism. The lowest values were found among pocket B mutants, most of which interacted strongly with tapasin, but otherwise there was no correlation between thermostability and tapasin interaction. Mutants resulting in increased hydrophobicity frequently acquired their maximal thermostability faster than those with increased polarity, suggesting that this process is largely driven by the thermodynamics of peptide binding. Folding, export, and tendency to misfold were influenced by polymorphism all along the peptide-binding site and were not specifically dependent on any particular region or structural feature. Frequent uncoupling of thermostability, folding/misfolding, and export can be explained by the distinct effect of mutations on the acquisition of a folded conformation, the optimization rate of B27-peptide complexes, and their quality control in the endoplasmic reticulum, all of which largely depend on the ways in which mutations alter peptide binding, without excluding additional effects on interactions with tapasin or other proteins involved in folding and export. The similarity of the generally disease-associated B*2707 to nondisease-associated subtypes in all the features analyzed suggests that molecular properties other than antigen presentation may not currently explain the relationship between HLA-B27 polymorphism and ankylosing spondylitis.HLA-B27 is the major susceptibility factor for a group of chronic inflammatory diseases known as spondyloarthropathies, whose prototype is ankylosing spondylitis (AS).2 This is a disorder characterized by inflammation of the entheses and joints of the axial skeleton, followed by pathological new bone formation, ultimately leading to ankylosis (1). HLA-B27 is involved in triggering the inflammatory process, but the mechanism is unknown. Four main hypotheses, each based on a particular property of HLA-B27, are currently being investigated. The arthritogenic peptide hypothesis (2) is based on the antigen-presenting specificity of HLA-B27 and assumes that molecular mimicry between microbial and self-derived B27 ligands would trigger autoimmune T cell cross-reaction and tissue injury. The misfolding hypothesis (3) is based on the slow folding and tendency to misfold of HLA-B*2705 (4) and assumes that accumulation of misfolded B27 heavy chain (HC) could trigger inflammation by eliciting the unfolded protein response and activation of NFB. The surface homodimer hypothesis (5, 6) is based on the expression of HC homodimers at the cell surface, following dissociation of HLA-B27-peptide complex...