The purpose was to test the effect of eccentric strength training and flexibility training on the incidence of hamstring strains in soccer. Hamstring strains and player exposure were registered prospectively during four consecutive soccer seasons (1999–2002) for 17–30 elite soccer teams from Iceland and Norway. The first two seasons were used as baseline, while intervention programs consisting of warm-up stretching, flexibility and/or eccentric strength training were introduced during the 2001 and 2002 seasons. During the intervention seasons, 48% of the teams selected to use the intervention programs. There was no difference in the incidence of hamstring strains between teams that used the flexibility training program and those who did not [relative risk (RR)=1.53, P=0.22], nor was there a difference compared with the baseline data (RR=0.89, P=0.75). The incidence of hamstring strains was lower in teams who used the eccentric training program compared with teams that did not use the program (RR=0.43, P=0.01), as well as compared with baseline data for the same intervention teams (RR=0.42, P=0.009). Eccentric strength training with Nordic hamstring lowers combined with warm-up stretching appears to reduce the risk of hamstring strains, while no effect was detected from flexibility training alone. These results should be verified in randomized clinical trials.