Muscle structure disorganization is a consequence of intense eccentric contractions, with symptoms that characterize exercise-induced muscle damage (EIMD). To date, few studies have described EIMD parameters at different muscle sites. The aim of the present study was to analyse indirect markers of EIMD at two elbow flexors sites over three days. Eleven healthy untrained men were submitted to a session of three sets of 10 eccentric elbow flexion repetitions on an isokinetic dynamometer. The isometric peak torque (PT), muscle soreness, elbow flexors oedema, (normalized muscle thickness [MT]) and echo-intensity (EI) were measured. There was a significant decrease in PT immediately after (Post) and 10 min, 24 h, 48 h and 72 h after intervention compared to that at baseline (p < 0 .05). MT% increased after 72 h compared with that immediately, 10 min and 24 h after intervention (p < 0.05). No statistical changes were observed in muscle soreness and oedema between the two muscle sites. With respect to EI%, significant differences were observed for the 24 h, 48 h and 72 h measures compared with those of the Post, 10 min and 24 h measures for both muscle sites; at the distal site, EI% was significantly higher than at the proximal site for measures after 24 h (p < 0.05). The presence of differences in EI% 24 h after eccentric training on distal sites of elbow flexors indicates non-uniform EIMD in this region.