Background Despite the widespread use of periodic health evaluation (PHE) to detect and prevent injury and illness in athletes, its effectiveness in detecting health conditions and relevant risk factors is still debated. Aim To assess health conditions detected by a comprehensive PHE in professional male football players and evaluate their consequences for participation clearance. Methods A total of 558 professional football players in Qatar completed a PHE prior to the 2013 or 2014 seasons: history, general medical (including blood test), cardiovascular (12-lead ECG and echocardiography) and a musculoskeletal examination, including a specific test battery targeting lower extremity strength and flexibility. On the basis of the PHE, players were either cleared or not cleared for participation. Results In 533 players (95.5%), at least one health condition was detected requiring treatment or follow-up. Vitamin D deficiency or insufficiency (≤30 ng/mL) was the most common medical condition (n=499, 89.4%), followed by hepatitis B non-immunity or infection (n=164, 29.4%). Cardiac screening identified 48 players (8.6%) with one or more abnormal findings (ECG (n=19, 3.4%) and echocardiography (n=14, 2.5%)). Musculoskeletal conditions were observed in 180 players (32.3%); injuries to or strength deficits of the hip/groin and thigh accounted for the largest proportion. Medical clearance was temporarily not given in 69 players (12.4%), while further examinations were being conducted. One player was disqualified from competitive football. Conclusions PHE revealed a high prevalence of health conditions requiring treatment or follow-up in professional footballers; however, only 12.4% of conditions impacted on final clearance for participation.