Electrophysiological recordings are considered a reliable method of assessing a person's alertness. The aim of this study was to show, firstly, that changes in alertness during a Reaction Time Test (RTT) can be determined with certain adaptive scoring stages but not with R&K scoring and secondly, that the different adaptive stages can explain findings in reaction time. In 17 male patients (50.8+/-9.7 years, Body-Mass Index (BMI) 31.9+/-5.1 kg/m2) diagnosed with Obstructive Sleep Apnea Syndrome (OSAS) (Respiratory Disturbance Index (RDI) 53.3+/-24.1 /h sleep) a 90 min daytime vigilance test was performed twice, after the diagnostic polysomnographic investigation and after two nights spent with nCPAP. After a computerised adaptive segmentation analysis, a visual rule-defined classification system categorised alertness into one of 12 adaptive scoring stages. 6 of the 12 stages are described by the alertness conditions comparable to WAKE and NREM1.4 stages are nearly classified as NREM2-4, Rapid Eye Movement (REM) and Movement Time (MT), and one stage reflects the increase of alertness from drowsiness. The typical stage of an alert subject increased significantly from a median of 65.9% before therapy to 80.8% in the second investigation. The percentages of clearly drowsy stages decreased significantly. In contrast, there were no significant changes in the percentages of sleep stages according to R&K criteria for both investigations. According to R&K criteria 178 of 398 failed reactions (Reaction time >10 s) occurred in stage WAKE. According to adaptive scoring, only 12 failed reactions appeared in the alert stage. During the other failed reactions the electrophysiological recordings showed decreases in alertness. Neither the visual assessment nor the descriptive statistical results of R&K scoring were helpful to interpret the patient's alertness condition. In contrast, the patients' increases in alertness with nCPAP could be described by the adaptive scoring stages. This method could be a very useful procedure, when an expert opinion is necessary. It also has an actual context to the discussion of the effectiveness of CPAP in the treatment of OSAS.