BACKGROUND: Hamstring injury is the single most common injury in European professional football and, therefore, time to return and secondary prevention are of particular concern. OBJECTIVE: To compare the effectiveness of two rehabilitation protocols after acute hamstring injury in Swedish elite football players by evaluating time needed to return to full participation in football team-training and availability for match selection. STUDY DESIGN: Prospective randomised comparison of two rehabilitation protocols. METHODS: Seventy-five football players with an acute hamstring injury, verified by MRI, were randomly assigned to one of two rehabilitation protocols. Thirty-seven players were assigned to a protocol emphasising lengthening exercises, L-protocol and 38 players to a protocol consisting of conventional exercises, C-protocol. The outcome measure was the number of days to return to full-team training and availability for match selection. Reinjuries were registered during a period of 12 months after return. RESULTS: Time to return was significantly shorter for the players in the L-protocol, mean 28 days (1SD±15, range 8-58 days), compared with the C-protocol, mean 51 days (1SD±21, range 12-94 days). Irrespective of protocol, stretching-type of hamstring injury took significantly longer time to return than sprinting-type, L-protocol: mean 43 vs 23 days and C-protocol: mean 74 vs 41 days, respectively. The L-protocol was significantly more effective than the C-protocol in both injury types. One reinjury was registered, in the C-protocol. CONCLUSIONS: A rehabilitation protocol emphasising lengthening type of exercises is more effective than a protocol containing conventional exercises in promoting time to return in Swedish elite football.