Atherosclerosis is a complex inflammatory disease in which oxidative stress is a major protagonist in the development and progression of the atherosclerotic plaque. All biochemical analysis studies of plaque over the past fifteen years have been carried out on whole plaque with no attempt to localise sites of differing biochemical conditions. This study set out to identify in oxidation levels and inflammatory markers in relation to spatial localisation within the plaque. Advanced plaque samples removed during endarectomy were obtained from the Christchurch Hospital Department of surgery and were dissected into 3-5 mm sections along the longitudinal axis prior to analysis. Samples were analysed for vitamin E, neopterin, total cholesterol and markers of oxidative damage to protein and lipids. Neopterin is a marker of inflammation as it is released by activated macrophages yet it has never been measured in plaques. Initial analysis showed that the acid precipitation method for removing protein from samples prior to HPLC neopterin analysis was causing a significant loss in neopterin. A new acetonitrile based protein removal procedure was developed. Markers of oxidative stress and inflammation where shown to vary across the length of an atherosclerotic plaque. This variation allows for localized incidences of high and low radical flux and microenvironments of depleted antioxidants or areas in which the prooxidative actions of molecular components are favoured. Significant correlations were rarely seen in more then one plaque and trends found in the combined data set generally did not hold true in individual plaques. This reflects upon the complexity of the disease, especially at this advanced stage in which the biochemical morphology of individual plaques is extremely diverse. Separation of the plaques into pre-, post-, and bifurcation areas did produce some trends. These can be related to shear stress variations in the blood flow; further investigations into the biochemical differences between these areas may provide a better understanding of the growth and development of the atherosclerotic plaque.