Background Acute hamstring re-injuries are common and hard to predict. The aim of this study was to investigate the association between clinical and imaging findings and the occurrence of hamstring re-injuries. Methods We obtained baseline data (clinical and MRI findings) of athletes who sustained an acute hamstring injury within 5 days of initial injury. We also collected data of standardised clinical tests within 7 days after return to play (RTP). The number of re-injuries was recorded within 12 months. We analysed the association between the possible predictive variables and re-injuries with a multivariate Cox proportional-hazards regression model. Results Eighty patients were included at baseline and 64 patients could be included in the final analysis because data after RTP were not available in 16 cases. There were 17 re-injuries (27%). None of the baseline MRI findings were univariately associated with re-injury. A higher number of previous hamstring injuries (adjusted OR (AOR) 1.33; 95% CI 1.11 to 1.61), more degrees of active knee extension deficit after RTP (AOR 1.13; 95% CI 1.03 to 1.25), isometric knee flexion force deficit at 15 after RTP (AOR 1.04; 95% CI 1.01 to 1.07) and presence of localised discomfort on hamstring palpation after RTP (AOR 3.95; 95% CI 1.38 to 11.37) were significant independent predictors of re-injury. Athletes with localised discomfort on hamstring palpation just after RTP were consequently almost four times more likely to sustain a re-injury. Conclusions The number of previous hamstring injuries, active knee extension deficit, isometric knee flexion force deficit at 15 and presence of localised discomfort on palpation just after RTP are associated with a higher hamstring re-injury rate. None of the baseline MRI parameters was a predictor of hamstring re-injury.