Purpose Cardiac and respiratory involvement constitutes serious complications of Duchenne muscular dystrophy (DMD). We hypothesized that obstructive sleep apnea syndrome (OSAS) may play a role in cardiac autonomic dysfunction in DMD. We sought to assess the presence of cardiac autonomic function in patients with DMD by analyzing heart rate variability (HRV) during polysomnography (PSG). Methods In a prospective study, all participants had whole-night PSG recorded and scored according to American Academy of Sleep Medicine guidelines. HRV analysis was performed on electrocardiography recordings from PSG recordings. Results Twelve consecutive males with DMD (mean age 9.0 +/- 3.1 years, mean BMI 20.6 +/- 4.8 kg/m2) and eight age-matched healthy males were enrolled. On clinical evaluation, 58% of patients with DMD had at least one symptom related to OSAS, such as snoring, witnessed apnea, or restless sleep. None of the controls had OSAS-related complaints. By PSG none of the controls had OSAS, while 42% of patients with DMD had OSAS (p= 0.004). Average R-R duration and mean percentage of successive R-R intervals > 50 ms values were significantly lower in patients with DMD than those in controls (p< 0.006). In patients with DMD and OSAS, LF/HF (low/high-frequency) ratio was significantly increased in NREM sleep compared with those in controls (p= 0.005). Higher apnea-hypopnea index and lower oxygen saturation showed significant correlations with higher LF power and LF/HF ratio (p< 0.001). Conclusion Cardiac autonomic dysfunction is present in DMD, being more pronounced in the presence of OSAS.