This study aimed to reveal the functional ability of functional movement screening (FMS) scores in determining an athlete's predisposition to injury. One hundred (50 females and 50 males) university level athletes, weight of 69.44 ± 5.84 kg, height of 172.69 ± 7.26 cm, age of 22.56 ± 2.99 years and Baecke score 21.66 ± 1.73, practised in football, handball and basketball sports (at least for 5 years), with no recent (<6 weeks) history of musculoskeletal injury were recruited. Of the 100 subjects, 35 of them suffered an acute, lower extremity (ankle = 20 and knee = 15 subjects) injury. An odds ratio was calculated at 4.70, meaning that an athlete has an approximately 4.7 times greater chance of suffering a lower extremity injury during a regular competitive season if they score less than 17 on the FMS. This study provides FMS reference values for university level athletes that will assist in the interpretation of individual scores when screening athletes for musculoskeletal injury and performance factors. More research is still necessary before implementing the FMS into a pre-participation physical examination for athletics, but due to the low cost and its simplicity to implement, it should be considered by clinicians and researchers in the future.