Nocturnal polysomnography (PSG) is the gold-standard to diagnose obstructive sleep apnoea syndrome (OSAS). However, it is complex, expensive, and time-consuming. We present an automatic OSAS detection algorithm based on classification of nocturnal oxygen saturation (SaO(2)) recordings. The algorithm makes use of spectral and nonlinear analysis for feature extraction, principal component analysis (PCA) for preprocessing and linear discriminant analysis (LDA) for classification. We conducted a study to characterize and prospectively validate our OSAS detection algorithm. The population under study was composed of subjects suspected of suffering from OSAS. A total of 214 SaO(2) signals were available. These signals were randomly divided into a training set (85 signals) and a test set (129 signals) to prospectively validate the proposed method. The OSAS detection algorithm achieved a diagnostic accuracy of 93.02% (97.00% sensitivity and 79.31% specificity) on the test set. It outperformed other alternative implementations that either use spectral and nonlinear features separately or are based on logistic regression (LR). The proposed method could be a useful tool to assist in early OSAS diagnosis, contributing to overcome the difficulties of conventional PSG.