Evidence came out showing that oxidative stress has a pivotal role in development and maintenance of inflammation and aberrant immune responses. Biomarkers of oxidative stress may define the proportion of oxidative damage underlying pathological conditions, and also foresee and monitor the possible efficacy of therapeutic strategies designed to control these pathologies. New compounds, which can be used as biomarkers, have been identified, and among them advanced oxidation protein products (AOPPs), formed mainly by chlorinated oxidants resulting from activity of myeloperoxidase. Our paper is aimed to review clinical evidences concerning the valuable potential of AOPPs as biomarkers of oxidative injury in development and progression of diseases and chronic conditions related to inflammatory status and immune dysregulation. These pathologies include metabolic syndrome, obesity, immune-mediated inflammatory diseases, neurodegenerative diseases, and cancer. Due to the heterogeneity of pathologies reported to be characterized by AOPP accumulation, it is evident that AOPPs are not merely a marker of neutrophil activation, but at the same time AOPPs cannot always be disease determinants. The data reported in this review corroborate the opinion that AOPPs can be successfully used to in vitro confirm the diagnosis of inflammatory and immune-mediated diseases, but at the same time evidence is that, very likely due to the way through which AOPPs are formed as well as the effect they can contribute to induce, AOPP values cannot be clearly reflective of their involvement in the pathogenesis and in the evolution of a specific disease.