Five atherosclerotic carotid and femoral plaques were sliced longitudinally. Each section was analysed for the concentrations of neopterin, α-tocopherol, TBARS, DOPA, dityrosine, protein carbonyl, protein and cholesterol. The spatial concentrations of the oxidative and inflammatory markers were diverse across and between the individual plaques suggested by the lack of consistent correlations and trends. The only correlation that occurred twice within the individual plaques was a positive correlation between α-tocopherol and cholesterol levels. In the combined plaque analysis which included data from eight previously studied plaques, neopterin, protein carbonyl and protein concentrations all had significant positive correlations and α-tocopherol concentrations positively correlated to cholesterol and negatively to TBARS. Thus overall the level of protein may influence protein carbonyl concentration and α-tocopherol may provide an antioxidant effect towards lipid peroxidation. Furthermore, the plaques were divided into three zones, pre-bifurcation, bifurcation and post-bifurcation, associated with shear stress levels. The neopterin concentrations were significantly high within the pre- and post-bifurcation region and the opposite trend occurred with the to peroxyl radical driven TBARS levels. The protein and cholesterol content in the postbifurcation was high, possibly due to the low and/or oscillatory shear stress occurring at these sites. The overall composition of the plaque, either thrombosed, heavily calcified or neither, also identified significant trends in marker concentrations between the plaques. The calcified plaques had significantly low levels of protein, cholesterol, α-tocopherol, DOPA and dityrosine whereas the thrombosed plaques had significantly high protein, α-tocopherol and dityrosine concentrations. The medication and symptoms presented by the patient had no major influence of the overall concentration of the markers within the plaques. Therefore even though individually the plaques have varied biochemical compositions, common influences were dictate the spatial and overall concentration of the markers within and across the plaques. Further potential markers were investigated for detection within plaque. AAS and GGS for replacement of the protein carbonyl assay as a more specific marker for protein oxidation, as well as the oxysterol 7-ketocholesterol detected simultaneously during α-tocopherol analysis. The 7-ketocholesterol would increase the information on lipid oxidation occurring in the plaque without increasing the volume of the limited homogenate required for the analysis. Investigation was also carried out on the mechanism of protein oxidation in human plasma that may provide mechanisms and interactions to protein oxidation within plaques.