The purpose of this study was to compare and analyze muscle function and EMG of the trunk and the lower extremity in short and long distance athletes and in order to determine difference in peak torque per unit weight, muscle power per unit weight, endurance ratio, and %MVIC classified by muscle. For that purpose, isokinetic muscle function tests for waist, knee, and ankle joints and EMG measurements for the trunk and the lower extremity muscle with running motion were conducted for 7 short and long distance high school athletes respectively. The study over muscle function of waist, knee, and ankle joints indicates that peak torque per unit weight of short distance athletes is higher than that of long distance athletes in extension and flexion of waist joint, plantar flexion of right ankle joint, and dorsi flexion of left ankle joint. In case of the muscle power per unit weight of short distance athletes is also higher than long distance athletes in waist, knee, and ankle joints. No difference in endurance ratio of waist, knee, and ankle joints between the two groups was founded. The results of the test over EMG of the trunk and the lower extremity show that %MVIC of erector spinae, rectus femoris, vastus medialis, vastus lateralis, and tibialis anterior is higher than that of long distance athletes in support phase. The above results proved to be the same in flight phase except for %MVIC of medial gastrocnemius. In other words, %MVIC of medial gastrocnemius for short distance athletes turned out to be higher than that of long distance athletes in flight phase.