Patients with obstructive sleep apnoea (OSA) have reduced event rates during slow wave sleep (SWS) compared with stage 2 sleep. To explore this phenomenon, ventilatory and arousal timing responses to partial and complete airflow obstruction during SWS versus stage 2 sleep were examined. Methods: Ten patients, mean±SD apnoea-hypopnoea index (AHI) 49.7±16.5 events/h with reduced OSA frequency during SWS (SWS AHI 18.9±14.0 events/h) slept with an epiglottic pressure catheter and nasal mask/pneumotachograph. Patients underwent rapid continuous positive airway pressure (CPAP) dialdowns to three subtherapeutic levels and brief airway occlusions in random order. Results: Post-dialdown, there were marked reductions in peak flow and minute ventilation, and progressive increases in inspiratory effort (p<0.001), but with limited ventilatory recovery and no differences between sleep stages. CPAP versus peak flow relationships on the third and second to last breath pre-arousal were not different between sleep stages. Arousals occurred later and post-dialdown arousal probability was lower during SWS compared with stage 2 sleep, Cox hazard ratio (95% CI) 0.65 (0.48 to 0.88), p=0.006. During SWS occlusions, time to arousal (mean±SEM) was prolonged (23.0±2.6 vs 17.1±1.7 s, p=0.02). Inspiratory effort developed more rapidly (-1.0±0.2 vs -0.6±0.1 cm H2O/s, p=0.019) and was more negative (-28.7±2.7 vs -20.3±1.6 cm H2O, p<0.001) on the breath preceding arousal. Conclusions: Except for a heightened ventilatory drive response during airway occlusion, airway function and ventilatory compensation to ventilatory challenge appear to be similar, but with consistently and substantially delayed arousal responses, in SWS versus stage 2 sleep.