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The development of skeletal deformities in seabream farming affects fish growth, survival, and production costs. Collagen distribution in different fish tissues might be correlated with swimming behavior. This study investigates whether scoliosis in seabreams is associated with changes to calcium-phosphor hydroxyapatite salts and collagen fibril morphology. Samples of decalcified vertebrae of scoliotic and non-scoliotic seabreams were examined with transmission electron microscopy and collagen micrographs were taken and analyzed. The mineral content, modulus of elasticity, and morphology of the vertebrae were also determined. The results indicated that fish with scoliosis had significant smaller mean vertebral collagen fibril diameters than the controls. Vertebrae in abdominal and caudal regions of the scoliotic seabreams appeared to be smaller than the respective vertebrae of the non-deformed seabreams. The calcium (Ca) and phosphorus (P) amounts of vertebrae of both scoliotic and non-scoliotic seabreams were not affected by the scoliosis deformity. The modulus of elasticity showed that the vertebrae from seabreams with scoliosis were more flexible than the vertebrae from seabreams without any skeletal deformity. The mechanical properties of bone are crucially dependent on collagen structure. Hence, how the vertebral column collagen of juvenile fish is related to the mechanism of deformities requires further investigation in order to provide a risk-reducing strategy to increase fish performance in aquaculture.