Objective Supervised exercise is currently recommended for the first-line treatment of intermittent claudication based on improvement in walking capacity. However, the promotion of skeletal muscle atrophy by repetitive ischemia-reperfusion caused by treadmill-based programs remains a concern. Because preservation of skeletal muscle mass (SMM) and lean mass (LM) is integral to functional capacity and longevity, this study measured the effect of standard treadmill-based supervised exercise on SMM and regional lower limb LM in patients with intermittent claudication. Methods Patients with calf claudication caused by infrainguinal peripheral artery disease underwent whole-body dual-energy X-ray absorptiometry scanning before and after completion of a 12-week supervised treadmill exercise program. Total body SMM and lower limb LM were measured according to anatomical regions of the lower limb (thigh vs calf) and side of symptoms. Walking performance was assessed using pain-free walking distance and 6-minute walking distance tests. Results Thirty-six patients with calf claudication completed exercise training and dual-energy X-ray absorptiometry scanning, allowing analysis of 55 symptomatic and 17 asymptomatic lower limbs. No difference in total body SMM (P = .41) or LM of symptomatic (P = .53) or asymptomatic calves (P = .59) was detected after the program. In contrast, a significant decrease in LM was observed in symptomatic (P = .04) and asymptomatic thighs (P = .005). Pain-free walking distance (P = .001) and the 6-minute walking distance both improved significantly (P = .004) but were not associated with changes in LM. Conclusions Twelve weeks of standard treadmill-training for intermittent calf claudication did not result in loss of calf LM; however, a significant decrease in bilateral thigh LM was observed, even in patients with unilateral symptoms. Further research on optimum exercise modalities and end points are required to determine the pathophysiology and effects of these changes on function and survival.