Background Epidemiological studies have mainly been performed on team sports. The authors set out to develop a protocol for large-scale epidemiological studies of injuries among elite athletics athletes.

Methods An argument-based method for investigation of complex design problems was used to structure the collection and analysis of data. Specification of the protocol was preceded by an examination of requirements on injury surveillance in individual sports and iterated drafting of protocol specifications, and followed by formative evaluations.

Results The requirements analysis shows that the central demand on the protocol is to allow for detailed epidemiological analyses of overuse injuries, which subsequently requires regular collection of self-reported data from athletes. The resulting study protocol is centred on a web-based weekly athlete e-diary enabling continual collection of individual-level data on exposure and injuries. To be able to interpret the self-reported data on injury events, collection of a wide range of personal baseline data from the athlete, including a psychological profile, is included in the protocol.

Conclusions The resulting protocol can be employed in intervention programmes that can prevent suffering among both adult elite and youth talent athletes who have made considerable life investments in their sport.