BACKGROUND Three hours per week of vigorous physical activity is found to be associated with reduced odds of sleep-disordered breathing. OBJECTIVE To investigate whether 12 weeks of high-intensity interval training (HIIT) reduced the apnoea-hypopnea index (AHI) in obese subjects with moderate-to-severe obstructive sleep apnoea. METHODS In a prospective randomised controlled exercise study, 30 (body mass index 37±6 kg/m2, age 51±9 years) patients with sleep apnoea (AHI 41.5±25.3 events/hour) were randomised 1:1 to control or 12 weeks of supervised HIIT (4×4 min of treadmill running or walking at 90%-95% of maximal heart rate two times per week). RESULTS In the HIIT group, the AHI was reduced by 7.5±11.6 events/hour (within-group p<0.05), self-reported sleepiness (Epworth scale) improved from 10.0±3.6 to 7.3±3.7 (between-group p<0.05) and maximal oxygen uptake improved from 28.2±7.4 to 30.2±7.7 mL/kg/min (between-group p<0.05) from baseline to 12 weeks. The AHI, self-reported sleepiness and VO2maxwere unchanged from baseline to 12 weeks in controls (baseline AHI 50.3±25.5 events/hour, Epworth score 5.9±4.3, maximal oxygen uptake 27.0±6.8 mL/kg/min). Body weight remained unchanged in both groups. CONCLUSIONS Twelve weeks of HIIT improved the AHI and self-reported daytime sleepiness in subjects with obese sleep apnoea without any change in the desaturation index and body weight.