Data on equine thoracic pathology hardly exist in breeds other than Thoroughbreds. To describe pathological changes of the osseous thoracic vertebral column in Warmblood horses, Shetland ponies and Konik horses, and to compare prevalence and severity. Descriptive post-mortem study. Computed tomography was used to examine the thoracic vertebral column of 34 Warmblood horses, 28 Shetland ponies, and 18 Konik horses. Osteoarthritis (OA), periarticular osteolysis, osseous cyst-like lesions and fragments of articular processes (APJs), costovertebral and costotransverse joints, soft tissue mineralisation surrounding these joints, intervertebral disc (IVD) mineralisation, impingement of spinous processes (SPs) and spondylosis were scored. APJ aplasia (98%; 58/59) occurred in 14 Shetland ponies. OA predominated in Warmblood horses across all joints (45% vs. 29 and 32%, p < 0.001). OA and periarticular osteolysis were found in particular in the costotransverse joints (p < 0.001) across all breeds. Warmblood and Konik horses had more and severe soft tissue mineralisation than Shetland ponies (2.3%, score 1.5 and 3.2%, score 1.3, respectively, vs. 0.3%, score 0.9, p < 0.01). Mid location was most often affected with highest severity score (4.2%, 1.5, p < 0.001). Konik horses displayed the highest IVD mineralisation (20%, p < 0.001), which notably increased with age (p < 0.001) compared with Warmblood horses (4.5%) and Shetland ponies (1.1%). SPs impingement was absent in Shetland ponies, and most prevalent in Warmblood horses (11.2%, p < 0.001) compared with Konik horses (2.2%). Osseous cyst-like lesions, fragments and spondylosis were minimal in all breeds and nearly absent in Shetland ponies. Clinical histories and macroscopic and histologic examinations were unavailable. Distinct breed differences exist in prevalence and severity of thoracic vertebral column osseous pathologies. Costotransverse joint pathology is more common than APJ pathology in all breeds. Warmblood horses are prone to OA, spondylosis and SPs impingement; Konik horses exhibit significant IVD mineralisation, and Shetland ponies demonstrate a high prevalence of APJ aplasia. Periarticular osteolysis, osseous cyst-like lesions, fragments and soft tissue mineralisation are notably low in Shetland ponies.