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We investigated the presence of radiographic thymus variants using a scoring system and examined their association with clinical and immunological features in primary Sjögren's syndrome (pSS) and polymyositis/dermatomyositis (PM/DM) patients. Cases of 72 patients with pSS and 47 with PM/DM were randomly selected from all visitors to our department who received chest CT scanning, excluding those with thymoma or thymic cyst, or age <30 years. We quantitatively interpreted and assessed thymus size and attenuation score in axial CT images. Thymic enlargement was identified in 16 (22.2%) pSS and 14 (29.8%) PM/DM patients. A thymus attenuation score ≥ 2 was seen in 11 (15.3%) pSS and 9 (19.1%) PM/DM patients. Thymic enlargement showed a significant association with the titre of rheumatoid factor in PM/DM patients. Thymic enlargement and score showed a significant association with body weight in pSS patients. Radiographic thymus variants are often observed in pSS and PM/DM patients, particularly in cases of PM/DM, and may suggest the role of an abnormal immune response in their pathogenesis.