Malformations in farmed fish are a prime research topic as it has a major impact on fish welfare and on the economical value of the product. In this study, the genetic component of spine deformities was estimated in European sea bass, a major species of Mediterranean aquaculture, with the use of a posteriori reconstruction of pedigree with microsatellites. Our population exhibited a very high malformation rate (81%), probably due to intense swimming of fish during pre-growing. The heritability of global spine deformities was evaluated to be 0.21 ± 0.04 on the underlying scale (0.33 ± 0.06 for lordosis, 0.13 ± 0.04 for scoliosis). Deformities scored by an internal or external examination turned out to be genetically the same trait (genetic correlations > 0.9), although phenotypic correlations were moderate to high (0.45 ± 0.04 to 0.92 ± 0.01) due to difficulties in scoring the less severe deformities. Along time (from 100 to 800 g mean weight), lordosis had a constant heritability, with very high genetic correlations between stages (> 0.9). Its incidence increased from 39 to 53% indicating that the malformation was probably present from the beginning of the rearing period but that its expression increased over time. A positive linkage between spine deformities and growth rate was demonstrated both by the higher early weight of affected fish and by the positive genetic correlation between weight and malformation (from 0.21 ± 0.15 to 0.40 ± 0.14), although deformities have a negative phenotypic impact on growth. However, heritabilities of malformation traits calculated here are only estimates that may indirectly describe the sensitivity of fish to the particular pre-growing environment as a function of different body weight genotypes. A quantification of realised heritability would therefore be necessary before concluding on the existence of a genetic basis for spinal malformations such as lordosis and scoliosis. Nevertheless and by precaution, selection for fast growth rate needs careful monitoring of deformities, and selection against malformations may counteract impacts of selection for fast growth.