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Abstract Background Lower extremity joint contractures have negative effects on gait in children with Duchenne muscular dystrophy (DMD). Thus, contracture prevention is essential for maintaining a patient’s functional ability and an acceptable quality of life. This study investigated hip flexion (HF), knee flexion (KF), and ankle joint plantar flexion (APF) contractures among male patients with DMD, based on the patients’ ambulatory status. Differences in major joint contractures, based on passive stretching exercise participation, were also investigated. Methods A total of 128 boys with DMD, followed at the DMD clinic of a tertiary care hospital, were included in this cross-sectional study. The passive ranges-of-motion of the hip, knee, and ankle joints were measured, in the sagittal plane, using a goniometer. The Vignos Scale was used to grade ambulatory function. Boys with DMD who performed stretching exercises for more than 5 min/session, > 3 sessions/week, were classified into the stretching group. Results The HF (23.5o), KF (43.5o), and APF (34.5o) contracture angles in the non-ambulatory group were more severe than those in the ambulatory group. APF contractures (41 patients, 52.6%) were more frequently observed early, even within the ambulatory period, than were hip (8 patients, 10.3%), and knee joint (17 patients, 21.8%) contractures. Passive stretching exercises > 3 sessions/week were not associated with the degree of lower extremity joint contractures in the ambulatory or non-ambulatory group. Conclusion HF, KF, and APF contractures are more common and severe when there is deterioration of ambulatory function. Stretching exercises alone are unlikely to prevent lower extremity joint contractures.