Hamstring injuries remain the most common injury type across many professional sports. Despite a variety of intervention strategies, its incidence in soccer players playing in the UEFA Champions League has increased by 4% per year over the last decade. Test batteries trying to identify potential risk factors have produced inconclusive results. The purpose of the current study was to prospectively record hamstring injuries, to investigate the incidence and characteristics of the injuries, and to identify possible risk factors in elite male soccer players, playing in the Kosovo national premier league. A total of 143 soccer players from 11 teams in Kosovo were recruited. To identify possible prevalent musculoskeletal or medical conditions a widespread health and fitness assessment was performed including isokinetic strength testing, Nordic hamstring strength test, functional tests, and a comprehensive anamnesis surveying previous hamstring injuries. On average 27.9% of the players sustained at least one hamstring injury with three players suffering bilateral strains with the re-injury rate being 23%. Injured players were significantly older and heavier and had a higher body mass index compared to non-injured ones (p < 0.05). There was a lower passing rate in the Nordic hamstring strength test and a higher injury incidence among the previously injured players compared to non-injured ones (p < 0.05). Except for hamstring/quadriceps ratio and relative torque at 60°/sec (p < 0.05) for dominant and non-dominant leg, there were no other significant differences in isokinetic strength regardless of the angular velocity. No differences were observed for functional tests between cohorts. Regression analysis revealed that age, Nordic hamstring strength test, previous injury history, and isokinetic concentric torque at 240°/sec could determine hamstring injuries by 25.9%, with no other significant predicting risk factors. The battery of laboratory and field-based tests performed during preseason to determine performance related skills showed limited diagnostic conclusiveness, making it difficult to detect players at risk for future hamstring injuries.