The progression of muscle damage was studied in the lower extremity and trunk muscles of patients with Duchenne muscular dystrophy (DMD) with a new quantitative computed tomography (CT) method. The degree of muscle fiber loss and fat tissue replacement was quantified using the indices of percent cross-sectional area (%CSA) of muscle and fat, or the percentages of the area having the CT numbers of normal muscle and fat. A cross-sectional study in 71 patients showed that as the disability stage progressed, both CT number and %CSA of muscle decreased while %CSA of fat increased. The rate of progression was different for each muscle, and the order of involvement was clarified. The CT findings were also significantly correlated with muscle strength, indicating validity of our method. Our findings of the natural course of muscle involvement would be useful in providing appropriate rehabilitative care as well as assessing the efficacy of therapeutic interventions.