Background: Screening of competitive athletes and other individuals exposed to regular and intense physical exercise, such as military personnel, can lead to an early and preclinical identification of cardiac conditions associated with a higher risk for sudden cardiac death. The electrocardiogram (ECG) has been recommended for the precompetitive screening, but its interpretation remains controversial. The aim of this study was to compare three different standardized criteria for interpretation of athletes’ ECG applied in military. Methods: Prospective study of 1,380 consecutive healthy military, 249 (18%) also involved in competitive sport, screened with clinical history, physical examination, and ECG. The ECG was interpreted according to the European Society of Cardiology (ESC) recommendations, the Seattle Criteria (SC), and the Refined Criteria (RC). Findings: Independently of the criteria used, the majority of the individuals included had ECG changes, mainly physiological: ESC 55.1%, SC 63.6%, and RC 64.4%. The rate of pathological ECGs was significantly higher with the ESC criteria when compared to SC and RC (ESC 14.8%, SC 5.0% and RC 4.5%; p < 0.001). A significant cardiac abnormality was diagnosed with additional investigations in 4 patients (Brugada syndrome Type 1, mitral valve prolapse, bicuspid aortic valve, and Wolff–Parkinson– White pattern). Discussion: Electrical cardiac adaptations are frequent in military personnel, similar to competitive athletes. Some ECG changes, previously considered pathological, could in fact correspond to physiological adaptations. The refinement of the ECG interpretation in this athletic population seems to reduce the rate of false-positive cases. This may have a favorable socioeconomic impact, especially by reducing the health cost burden and number of disability days.