Tissue ischemia is a major cause of morbidity contributing to disease processes such as cardiovascular diseases, stroke, cancer, and traumatic injury and may lead to death. Failure to quickly reestablish flow to ischemic tissue results in tissue death. However, even timely return to normal flow has a downside in that the reintroduction of oxygen to ischemic tissue results in ischemia/reperfusion (I/R) injury that produces an oxidant stress. This pathological process requires new therapeutic strategies and agents to reduce the personal, social and economic loss. One of the most generally accepted mechanisms for the pathology of I/R injury is the production of the reactive oxygen species (ROS), suggesting antioxidants may ameliorate I/R injury. Caffeic acid phenethyl ester (CAPE), a plant derived polyphenolic compound, has been shown to protect organs from I/R induced damage in vivo, and this effect has been attributed to its antioxidant activity. To better understand the mechanism of CAPE protection, a model using menadione-induced oxidative stress in human endothelial cells to simulate I/R injury in vitro was developed. Gene expression analysis was performed with microarrays undergoing cytoprotection with CAPE. The dose-dependent cytoprotection of CAPE has been related to its induction of heme oxygenase-1 (HO-1). With the aim of improving the beneficial effect of CAPE and understanding structure activity relationship, six new catechol ring-fluorinated CAPE derivatives were synthesized and evaluated in the menadione-endothelial cell model. The data suggest good cytoprotective effects of CAPE and some analogues and indicate important structural features for cytoprotection. Further investigation of the mechanism of cytoprotection showed that cytoprotection profiles of CAPE and derivatives correlate better to their ability to induce HO-1 in human endothelial cells than free radical scavenging activity. One CAPE derivative (FCAPE) with cytoprotective effects similar to CAPE in vitro exhibited better stability in rat plasma. A validated ultra-performance liquid chromatography/tandem mass spectrometric method was developed that allowed for quantification of CAPE and FCAPE in plasma samples. Pharmacokinetic studies in male Sprague Dawley rats following intravenous bolus administration of 5, 10, and 20 mg/kg CAPE and 20 mg/kg FCAPE were performed. The results indicate that dose proportionality for CAPE does not exist in the dose range studied. Although the elimination half life was found not to be significant different between CAPE and FCAPE, significant difference was observed between the total body clearance of FCAPE and CAPE which may due to the difference in volume of distribution.