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Objectives Anatomical variation of the sacroiliac (SI) joints is common and specific variants are associated with erosions and bone marrow oedema on imaging. Our investigation aims to evaluate whether anatomical variations influence the clinical presentation of axial spondyloarthritis (axSpA).Methods In this propensity score matched post hoc analysis documented clinical data from four prospective clinical cohorts was assessed. Classification of back pain as inflammatory (=IBP), human leucocyte antigen-B27 positivity, family history, disease activity according to Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), symptom duration, elevated acute phase reactants, peripheral and extramusculoskeletal manifestations were evaluated. Statistical analyses were done using (generalised) linear models, t-tests, χ2 tests and analysis of variances. Multiple testing was corrected according to Bonferroni.Results A total of 165 patients (86 women) were included. Atypical SI joints, defined by the presence of accessory joint facets, iliosacral complex or crescent-shaped ilii on MRI, were identified in 61 out of 165 patients with axSpA. Disease activity, assessed by BASDAI and symptom duration were similar in both groups (adjusted ß=−0.118 (95% CI -0.713, 0.476), p=0.696 and 120.0 (107.4) vs 116.5 (98.3) months, p=0.838, respectively). There was no significant difference in IBP between the groups (adjusted OR=0.614 (95% CI 0.274, 1.377), p=0.236). Sex-stratified analysis revealed no statistically significant results.Conclusion Our analysis suggests that clinical phenotypes do not significantly differ between patients with axSpA with and without atypical joints.