Using heart rate spectral analysis of nocturnal pulse oximetry, we prospectively evaluated the utility of this methodology in patients clinically suspected of having obstructive sleep apnoea (OSA). A hundred and ninety-seven outpatients referred with symptoms compatible with the diagnosis of OSA were studied. All participants had nocturnal pulse oximetry performed simultaneously with conventional polysomnography. Power density of heart rate obtained by nocturnal pulse oximetry was analysed using fast Fourier transformation of a Hamming-windowed signal. Recording test results were classified as abnormal (suspicion of OSA) in the presence of a peak in the periodogram between period boundaries 30-70 sec. A normal test result was defined as the absence of the 30-70 sec peak in the periodogram. The total area of the periodogram (S(TOT)), the area enclosed in the periodogram between the period boundaries 30-70 sec (S(30-70)), the area enclosed in the period boundaries 30-70 sec with respect to the total area of the periodogram (S) and the peak amplitude 30-70 sec (PA) were measured. The presence of a peak in the periodogram has a sensitivity of 81.3%, a specificity of 91.5% a positive predictive value of 89.1% and a negative predictive value of 85.1% for OSA diagnosis. The OSA patients were found to have higher values of S(TOT), S(30-70), S and PA than the non OSA patients. Receiver operating characteristics (ROC) curve was constructed at different thresholds of S(TOT), S(30-70) S and PA. For a PA threshold of 10(%)2, heart rate spectra analysis sensitivity for OSA was 58% and specificity was 92%. Furthermore, the positive and negative predictive values for diagnosis of OSA were 87 and 72% respectively. Apnoea hypopnea index (AHI) correlated significantly with S(TOT) (r=0.44; P<0.001), S(30-70) (r=0.59: P<0.001), S (r=0.58; P<0.001) and PA (r=0.58; P<0.001). According to our results, heart rate spectral analys s obtained by nocturnal pulse oximetry and identification of peak in the periodogram between period boundaries 30-70 sec could be useful as a diagnostic technique for OSA patients.