Skeletal malformations in farmed fish are a major problem in aquaculture, not only for economic losses that can generate the maintenance of deformed fish, but also by the physiological and morphological implications in fish along life cycle. These malformations may be starting from the earliest stages of development and be associated with a degeneration of the bone structure with age, or genetic, nutritional, environmental factors and management, or relate to each other, making difficult to determine a single causative agent. The present critical review summarizes existing information on type, occurrence and possible causative factors associated with skeletal malformations with particular emphasis on cranial malformations.