Many exercise models have demonstrated associations between eccentric muscle actions and muscle damage. However, the magnitude of muscle damage varies among the models. It appears that responses to eccentric exercise are different between leg and arm muscles but this has not been systematically clarified. This study compared leg and arm eccentric exercises of the same relative intensity for indices of muscle damage. Eleven healthy untrained males [Age: 21.2 (1.0) years, Height: 179.4 (3.0) cm, Weight: 78.4 (3.1) kg] performed a sub-maximal eccentric exercise of the knee extensors (LEGS) and the elbow flexors (ARMS), separately. Both LEGS and ARMS consisted of six sets of 12 repetitions with an intensity corresponding to 75% of the predetermined maximal eccentric peak torque (EPT) of each muscle. Range of motion (ROM), delayed onset muscle soreness (DOMS), serum creatine kinase (CK) and lactate dehydrogenase (LDH) activities, myoglobin (Mb) concentration, and muscle strength [EPT and isometric peak torque (IPT)] were assessed before and 24, 48, 72, and 96 h following exercise. Significant (P < 0.05) changes in DOMS and ROM were observed up to 96 h after both exercise bouts, and the magnitude of the change was similar between LEGS and ARMS. Increases in CK and Mb were significantly (P < 0.05) larger after ARMS than LEGS at 72 and 96 h post-exercise. EPT and IPT were significantly (P < 0.05) lower than the baseline up to 96 h post-exercise for ARMS but were fully recovered by 96 h post-exercise for LEGS. Decreases in muscle strength were significantly (p < 0.05) larger following ARMS than LEGS at 48, 72, and 96 h post-exercise for EPT, and from 24 h to 96 h post-exercise for IPT. These results suggest that the magnitude of muscle damage is greater and the recovery of muscle function was slower after eccentric exercise of arm elbow flexors than the knee extensors.