Aim: The objective of this study was to assess a new lead system method to improve electrocardiographic measurement in horses. Materials and Methods: Twenty-two horses with an average age of 8.8±0.8 years were enrolled in this study. Horses were divided into two groups, consisting of a control group (n=11) and athlete group (n=11). Electrocardiography (ECG) and echocardiography were performed to provide information on the structure and function of the heart. Two lead systems, base apex and modified precordial leads, were used for the electrocardiogram to assess the cardiac electrophysiological functions. Results: PR interval, QT interval, and QRS-T angle presented significant differences between the control and athlete groups when the modified precordial lead system was used. However, significant variations in the mean electrical axis were found when the base apex lead system was used. The modified precordial lead system resulted in more significant differences in cardiac electrophysiological parameters than the base apex lead system. In the athlete group, echocardiography showed cardiac adaptations such as increases in the left atrial and left ventricular dimensions and stroke volume and a decrease in heart rate in response to exercise and training. The observed differences in cardiac morphology and function between groups suggested differences in health performance in the athlete group. Conclusion: These data provided the first evidence that the modified precordial lead system improved statistical variation in ECG recording and provided the most reliable method for health screening in horses.