All 12 female football clubs (228 players) and 11 of 14 male clubs (239 players) in the Swedish premier league were followed prospectively during the 2005 season. Individual exposure (playing time), injuries (time loss), and injury severity (days lost due to injury) were recorded by the team medical staffs. Injury incidence was higher for male players during both training (4.7 vs 3.8 injuries/1000 h, P=0.018) and match play (28.1 vs 16.1, P<0.001). However, no difference was found in the incidence of severe injury (absence >4 weeks) (0.7/1000 h in both groups). The thigh, especially the hamstrings, was the overall most commonly injured region in both sexes, while the hip/groin was more commonly injured in male players and the knee in female players. Knee ligament injuries accounted for 31% and 37% of the total time lost from football for male and female players, respectively. In conclusion, male elite players had a higher injury incidence than their female counterparts although no difference was observed in the incidence of moderate to severe injury. We recommend that preventive measures should be focused on hamstring and knee ligament injury in order to reduce the overall injury burden.