Background: The prevalence of obstructive sleep apnoea (OSA) is high in patients with hypertrophic cardiomyopathy. The effect of septal myectomy on OSA is not clear. This study aimed to examine the association between hypertrophic obstructive cardiomyopathy and OSA before and after septal myectomy. Method: We included 85 consecutive patents with a confirmed diagnosis of hypertrophic obstructive cardiomyopathy who underwent septal myectomy. Polysomnography was performed in all patients before and 3 months after the surgery. Results: Of the 85 patients, 49 (58%) were diagnosed with OSA. Patients with OSA were significantly older than those without OSA. The incidence of atrial fibrillation significantly increased during the perioperative period in patients with OSA (p = 0.03). The severity of OSA significantly increased 3 months after surgery, as determined by the apnoea–hypopnea index (AHI; p < 0.001), obstructive apnoea index (p = 0.024), and hypopnoea index (p = 0.003), whereas central apnoea index was decreased (p = 0.008). In the multivariate linear regression analysis, mean oxygen desaturation and time% with SpO2 <90% during sleep before surgery were significantly associated with increased AHI, independently of body mass index and sex (p = 0.026 and p = 0.007, respectively; adjusted R2 = 0.365). Conclusions: The severity of OSA significantly increased 3 months after septal myectomy as determined by AHI, obstructive apnoea index, and hypopnoea index. Mean oxygen saturation and time% with SpO2 <90% during sleep before surgery were independently associated with the increase of AHI. However, the specific mechanism of such deterioration of OSA after septal myectomy needs to be determined in detail. © 2019 Australian and New Zealand Society of Cardiac and Thoracic Surgeons (ANZSCTS) and the Cardiac Society of Australia and New Zealand (CSANZ)