Sleep apnea-hypopnea syndrome (SAHS) is significantly underdiagnosed and new screening systems are needed. The analysis of oxygen desaturation has been proposed as a screening method. However, when oxygen saturation (SpO(2)) is used as a standalone single channel device, algorithms working in time domain achieve either a high sensitivity or a high specificity, but not usually both. This limitation arises from the dependence of time-domain analysis on absolute SpO(2) values and the lack of standardized thresholds defined as pathological. The aim of this study is to assess the degree of concordance between SAHS screening using offline frequency domain processing of SpO(2) signals and the apnea-hypopnea index (AHI), and the diagnostic performance of such a new method. SpO(2) signals from 115 subjects were analyzed. Data were divided in a training data set (37) and a test set (78). Power spectral density was calculated and related to the desaturation index scored by physicians. A frequency desaturation index (FDI) was then estimated and its accuracy compared to the classical desaturation index and to the apnea-hypopnea index. The findings point to a high diagnostic agreement: the best sensitivity and specificity values obtained were 83.33% and 80.44%, respectively. Moreover, the proposed method does not rely on absolute SpO(2) values and is highly robust to artifacts.