A rapid and sensitive method to determine 8-oxoguanine (8oxoG) and 8-hydroxydeoxyguanosine (8OHdG), biomarkers for oxidative DNA damage, in cerebral cortex microdialysate samples using capillary electrophoresis (CE) with electrochemical detection (CEEC) was developed. Samples were concentrated on-column using pH-mediated stacking for anions. On-column anodic detection was performed with a carbon fiber working electrode and laser-etched decoupler. The method is linear over the expected extracellular concentration range for 8oxoG and 8-OHdG during induced ischemia-reperfusion, with R.S.D. values <or=5% and limit of detection of 0.5 nM for both analytes. Basal concentrations of 8oxoG in rat cerebral cortex microdialysate were determined to be 3.2+/-0.6 nM. Actual 8oxoG concentration in the brain was estimated to be 5.5+/-1.3 nM based on in vivo delivery probe calibration. 8OHdG was not detected under basal conditions in the rat cerebral cortex extracellular fluid (ECF). These results were confirmed by LC with tandem mass spectrometry.