The present review sums up and discusses the current literature on occurrence, causation and pathology of vertebral deformities in farmed Atlantic salmon, and also gives a brief introduction into the normal ontogeny and anatomy of the vertebral column of Atlantic salmon. Skeletal development and growth are sensitive processes that can be affected by many factors. Many of these factors can be manipulated under farming conditions, and are thus regarded as risk factors. Several risk factors that relate to environmental conditions and to feed composition have been identified. Elevated temperatures and photoperiod manipulation to speed up growth are likely the most important environmental factors that cause skeletal deformities. Among the nutritional factors, optimal phosphorus nutrition during specific periods, for example after transfer to sea water, appears to be critical for development of deformity at later stages. More research is needed to understand the interdependency of genetics, development, aging, phosphorus nutrition, temperature and photoperiod, in order to establish the best practice procedures for salmon farming that improve fish welfare.