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Auto-adjusting positive airway pressure (APAP) devices are being increasingly used to treat obstructive sleep apnoea (OSA). Anecdotal encounters of obese patients requiring high therapeutic pressure whose OSA was inadequately controlled by APAP led to this study aiming to compare the effectiveness of continuous positive airway pressure (CPAP) and APAP (S8 Autoset II(®) , ResMed, NSW, Australia) in a randomised, single-blinded crossover trial. Twelve morbidly obese patients with severe OSA [mean±SD apnoea-hypopnoea index (AHI) 75.8±32.7, body mass index 49.9±5.2 kg m(-2) , mean pressure 16.4 cmH(2)O] were consecutively recruited, and received CPAP or APAP in random order for six nights at home, separated by a four-night washout. Polysomnographic (PSG) indices of OSA were recorded at baseline and following each treatment arm. Both therapies substantially reduced the AHI (APAP 9.8±9.5 and CPAP 7.3±6.6 events h(-1) ; P=0.35), but residual PSG measures of disease (AHI5) were common. APAP delivered a significantly lower 95th percentile pressure averaged over the home-use arm than CPAP (14.2±2.7 and 16.1±1.8 cmH(2)O, respectively, P=0.02). The machine-scored AHI significantly overestimated the level of residual disease compared with the laboratory-scored AHI (using Chicago criteria); however, when the machine-scored AHI was ≤5 and ≤10 this was always confirmed by the PSG data. In morbidly obese OSA patients without significant co-morbid disease requiring high therapeutic pressure, our data provide support for the use of either APAP or manually titrated CPAP. We recommend objective assessment by sleep study if the S8 Autoset II indicates a high level of residual disease.