Sleep apnoea is associated with chronic kidney diseases. A high obstructive sleep apnoea (OSA) prevalence is shown in patients with hypertrophic cardiomyopathy (HCM). Whether the presence of OSA would affect the renal function of patients with HCM is unknown. Forty-five consecutive patients with HCM were divided into the HCM OSA- and OSA+ groups. Forty-three patients with OSA without HCM were recruited as controls. Clinical indices, including estimated glomerular filtration rate (eGFR) and urine 8-hydroxy-2-deoxyguanosine (8-OHdG), were measured. The eGFR was significantly lower in the HCM OSA+ group than in the HCM OSA- (P < 0.05) and OSA (P < 0.001) groups. Multivariate linear regression analysis identified that the apnoea-hypopnoea index was independently associated with eGFR in all patients with HCM (β = -1.329, 95% confidence interval: -1.942, -0.717, P < 0.001). The urine 8-OHdG level, an oxidative stress marker, was significantly higher in the HCM OSA+ group than in the HCM OSA- (P < 0.001) and OSA (P < 0.001) groups and significantly correlated with the AHI (r = 0.467, P = 0.003) and eGFR (r = -0.457, P = 0.004) in all patients with HCM. Our study suggests a risk of eGFR decline in patients with HCM and OSA.