Football is one of the most popular sports worldwide. Unfortunately, football players are highly exposed to injuries and muscle injuries are the most common ones. The aim was to study possible differences of muscle injuries regarding type, localization and the extent of injury between the dominant and non-dominant leg in elite male football players. Another aim was to study the injury incidence of muscle injuries of the lower extremity during match and training. Data were consecutively collected between 2007 and 2013 in a prospective cohort study based on fifty-four football players from one team of the Swedish first league. The injury incidence was calculated for both match and training and injuries to the hip adductors, quadriceps, hamstrings and triceps surae were diagnosed and evaluated with ultrasonography and their length, depth and width were measured to determine the extent of structural muscle injuries. Fifty-four players suffered totally 105 of the studied muscle injuries. Out of these 105 injuries the dominant leg was affected in 53% (n=56) of the cases. A greater extent of the injury was found in the dominant leg when compared to the non-dominant leg with regards to structural injuries of the hamstrings. No other significant differences were found. Structural hamstring muscle injuries were found to be of greater extent in the dominant leg when compared to the non-dominant leg. This new finding should be taken into consideration when allowing the football player to return to play after leg muscle injuries.