Obstructive Sleep Apnea Syndrome (OSAS) is characterized by desaturation in blood oxygen level and sleep fragmentation because of repeated upper airway obstruction. Auditory Event related potentials (AERPs) are scalp recorded voltage fluctuations, which reflect several cognitive processes generated within specific brain regions during auditory stimulus processing. In this study, we aimed to investigate cognitive deficits in OSAS patients with AERPs by taking the effects of aging factor into consideration. AERPs were recorded using an auditory oddball paradigm from 27 OSAS patients (range 28 to 67 years old) and 29 healthy control subjects (range 23 to 60 years old) participated in the study. To evaluate the effects of aging, both the OSAS patients and the controls were divided into two age groups: younger (<45 years) and older (≥45 years). Amplitudes and latencies of N100, P200, N200 and P300 responses to oddball target stimuli were analyzed by repeated measures analyses of variance (ANOVA). Statistical analyses indicate that the P300 amplitudes were lower (P < 0.001), and P300 latencies were longer (P < 0.001) in OSAS patients. However, AERPs when analyzed according to age groups: P300 latencies were significantly longer in both younger and older OSAS patients (P < 0.05) but P300 amplitudes were not different in older OSAS patients compared to controls (P > 0.05). Our results suggest that negative effects of OSAS on cognitive functions could be observed with event-related brain responses. Changes in the P300 latencies are more robust evidence than other AERP components in evaluating cognitive deficits in OSAS patients.