To implement an injury recording protocol in a junior elite Australian Football competition and determine the injury profile of this population.Longitudinal cohort study.Players from an elite Under 18 Australian Football competition were tracked throughout one football season in terms of participation or non-participation in the football competition. Injury reporting forms were collected for all players who were not available for selection as a result of injury.The cohort consisted of 532 players who provided consent for inclusion in the study (100% of players in the competition). There were 256 injuries sustained during the season. Results were standardised to a 40 man team to allow comparison with results from the Australian Football League. The injury incidence was 17.1 new injuries per club (95% CI 14.1-19.4), and prevalence 63.3 missed matches per club (95% CI 59.1-67.1). The category "Ankle joint injuries" was the most commonly reported (n=34) and "Collision with another player" was the main injury mechanism (n=75).The most commonly injured region in junior elite Australian Football was the ankle and collision with another player was the most common injury mechanism. As with previous reports on junior Australian Football, injury incidence was low in comparison to the senior elite competition. Defining the injury profile guides injury prevention strategies. Analysis of injury in junior elite football may provide a unique opportunity to affect both junior and senior injury rates.