To confirm validity of the Self-administered Comorbidity Questionnaire modified for patients with SpA (mSCQ), and assess whether validity improves when adding items on extra-articular manifestations (EAMs), i.e. uveitis, psoriasis, and IBD, and osteoporosis and fractures. Data from the Assessment in SpondyloArthritis international Society COMOrbidities in SPondyloArthritis study were used. Criterion validity of presence of EAMs, osteoporosis and fractures was assessed as agreement (kappa) between patients' self-reported and physician-confirmed disease. Construct validity of the mSCQ including EAMs, osteoporosis and/or fractures (SpA-SCQ) was assessed by testing hypotheses about correlations with demographics, physical function, work ability, health utility and disease activity, and was compared with construct validity of the rheumatic disease comorbidity index. In total, 3984 patients contributed to the analyses. Agreement between patient-reported and physician-reported EAMs was substantial to almost perfect (uveitis ĸ = 0.81, IBD ĸ = 0.73, psoriasis ĸ = 0.86). Agreement for osteoporosis (ĸ = 0.38) and fractures (ĸ = 0.39) was fair. As hypothesized, the mSCQ correlated moderately to weakly with age, physical function, work limitations and health utility, and very weakly with disease activity. In contrast to our hypothesis, adding EAMs, osteoporosis and/or fractures to the mSCQ decreased correlations with several external constructs, especially among patients with peripheral SpA. Correlations with the different constructs were stronger for the both mSCQ and SpA-SCQ (rBASFI = 0.34; rEQ-5D = -0.33) compared with the rheumatic disease comorbidity index (rBASFI = 0.24; rEQ-5D = -0.21). The mSCQ is a valid self-report instrument to assess the influence of comorbidities on health outcomes in patients with SpA. Adding EAMs and/or osteoporosis or fractures does not improve validity of the mSCQ. © The Author(s) 2019. Published by Oxford University Press on behalf of the British Society for Rheumatology.