A number of mass strandings of beaked whales have in recent decades been temporally and spatially coincident with military activities involving the use of midrange sonar. The social behaviour of beaked whales is poorly known, it can be inferred from strandings and some evidence of at-sea sightings. It is believed that some beaked whale species have social organisation at some scale; however most strandings are of individuals, suggesting that they spend at least some part of their life alone. Thus, the occurrence of unusual mass strandings of beaked whales is of particular importance. In contrast to some earlier reports, the most deleterious effect that sonar may have on beaked whales may not be trauma to the auditory system as a direct result of ensonification. Evidence now suggests that the most serious effect is the evolution of gas bubbles in tissues, driven by behaviourally altered dive profiles (e.g. extended surface intervals) or directly from ensonification. It has been predicted that the tissues of beaked whales are supersaturated with nitrogen gas on ascent due to the characteristics of their deep-diving behaviour. The lesions observed in beaked whales that mass stranded in the Canary Islands in 2002 are consistent with, but not diagnostic of, decompression sickness. These lesions included gas and fat emboli and diffuse multiorgan haemorrhage. This review describes what is known about beaked whale anatomy and physiology and discusses mechanisms that may have led to beaked whale mass strandings that were induced by anthropogenic sonar. Beaked whale morphology is illustrated using Cuvier’s beaked whale as the subject of the review. As so little is known about the anatomy and physiology of beaked whales, the morphologies of a relatively well-studied delphinid, the bottlenose dolphin and a well-studied terrestrial mammal, the domestic dog are heavily drawn on.