Objective: Presence of a biochemical marker of cerebral injury would be of great benefit in obstructive sleep apnea syndrome (OSAS) to screen for even small brain damage and to monitor efficacy of therapy. The aim of this study was to evaluate whether two different parameters in serum, neuron-specific enolase (NSE) and homocysteine, can be used to detect even subtle levels of cerebral injury in OSAS patients. Material and Methods: We studied 38 patients with OSAS and 30 control subjects with an apnea-hypopnea index (AHI) less than five events per hour. All were evaluated by full-night polysomnography, and in the following morning, serum levels of NSE and homocysteine levels were measured using standard techniques. Results: The AHI in OSAS group was 39.2 +/- 13.8 (mean +/- SD) AH/h. Serum NSE levels were significantly higher in OSAS group (12.3 +/- 5.0 ng/ml) than in the control group (8.2 +/- 1.9 ng/ml; p< 0.01). No significant difference was detected between the groups with regard to serum homocysteine levels (14.1 +/- 6.3 v 14.6 +/- 4.8 mu mol/L; p> 0.05). Conclusion: Elevated serum NSE levels were much more correlated with the severity of OSAS, whereas homocysteine levels were in normal range in these OSAS cases who were otherwise healthy. We believe that there is a need for more sensitive biochemical markers and methods for detecting small cerebral injury in patients with sleep apnea syndrome.