Oxidative damage is a naturally occurring process where reactive oxygen species (ROS) attack and disrupt normal cellular function; however, these effects become elevated during a stress event, such as ischemia/reperfusion or seizure. One result of oxidative stress is lipid peroxidation, where ROS attack free unsaturated fatty acids forming lipid hydorperoxides, which then break down to form secondary products acrolein, 4-hydroxynonenal, and malondialdehyde (MDA) resulting in irreversible membrane damage and ultimately cell death. Described here is a CE-fluorescence method for the determination of MDA in conjunction with in vivo microdialysis sampling. MDA was derivatized with thiobarbituric acid under acidic conditions for 20 minutes and injected directly into the capillary without any pretreatment. This method provided a limit of detection of 25 nM (S/N=3) and a linear range of 25-2400 nM (1.8-174 ng/mL). This method was used to quantify MDA in rat heart, muscle, liver, and brain dialysate.