In this paper, we explored the link between sleep apnoea and cardiovascular disease (CVD) using a time-series statistical measure of sleep apnoea-related oxygen desaturation. We compared the performance of a hypoxic measure derived from the polysomnogram with the Apnoea Hypopnoea Index (AHI) in predicting CVD mortality in patients of the Sleep Heart Health Study.We estimated the relative cumulative time of SpO2 below 90% (Tr90) using pulse oximetry signals from polysomnogram recordings as the hypoxic measure of desaturation patterns. Then, the survival curves for hypoxia quintiles were evaluated for the prediction of CVD mortality and were compared with the results using AHI for prediction. We also calculated the Cox hazard ratios for Tr90 and AHI. Our results show that the Tr90 was a better predictor of CVD mortality outcomes than AHI.