This review focuses on the structural and functional changes occurring in respiratory as well as peripheral muscles in COPD patients. These changes are particular for each muscle territory or compartment. Respiratory muscles predominantly undergo structural adaptive changes. However, they have to do their job in unfavourable mechanical conditions and thus their function is impaired. Peripheral muscles have to be grouped in at least two different compartments: upper and lower limb muscles. The structure and function are relatively preserved in the former, due to the maintenance of some daily activities involving the arms or even the use of some of these muscles in the ventilatory effort. Lower limb muscles in contrast undergo involute structural changes which result in an impairment in their function and in the global exercise capacity of the individual. Deconditioning due to a reduction in daily activities secondary to ventilatory impairment is probably the driving factor for these changes. Although the level of activity appears to be the main determining factor in changes occurring in different territories, this would be modulated by other local and systemic factors, such as inflammation, oxidative stress, drugs and nutritional abnormalities.