Abstract Objectives The primary objective was to compare the clinical characteristics of SpA patients with and without root joint disease (RJD+ and RJD–). The secondary objectives were to compare the prevalence of RJD across various SpA subtypes and in different world regions, and to compare the SpA axial severity and SpA burden between RJD+ and RJD–. Methods This is a post hoc analysis of the Assessment of Spondyloarthritis International Society PerSpA study (PERipheral involvement in SpondyloArthritis), which included 4465 patients with SpA [axial (axSpA), peripheral (pSpA), PsA, IBD, reactive and juvenile] according to the rheumatologist’s diagnosis. RJD was defined as the ‘ever’ presence of hip or shoulder involvement related to SpA, according to the rheumatologist. Patient characteristics were compared between RJD+ and RJD–. Multivariable stepwise binary logistic regression analyses were conducted to identify factors associated with ‘RJD’, ‘hip’ and ‘shoulder’ involvement. Results RJD was significantly associated with the SpA main diagnosis (highest in pSpA), a higher prevalence of HLA-B27 positivity, enthesitis, tender and swollen joints, CRP, conventional synthetic DMARDs, loss of lumbar lordosis and occiput-wall distance >0. RJD was more prevalent in Asia, and occurred in 1503 patients (33.7%), with more hip (24.2%) than shoulder (13.2%) involvement. Hip involvement had a distinct phenotype, similar to axSpA (including younger age at onset, HLA-B27 positivity), whereas shoulder involvement was associated with features of pSpA (including older age at onset). Conclusion RJD+ SpA patients had a distinctive clinical phenotype compared with RJD–. Hip involvement, based on the rheumatologist’s diagnosis, was more prevalent than shoulder involvement and was clinically distinct.