Propensity to diabetic nephropathy (DN), retinopathy (DR), and cardiovascular disease (CVD) varies between individuals. Current biomarkers such as indicators of glycemia (HbA1c), retinal examinations, and albuminuria, cannot detect early tissue damage. HbAIc also doesn’t reflect most glycative and oxidative chemical pathways that cause complications, and studies of new biomarkers to measure their end-products are needed. This review proposes the study of advanced glycation end products (AGEs) and oxidation end-products (OPs) in long-term diabetes outcome studies. AGEs integrate the activity of glycation pathways that form dicarbonyls, while OPs reflect superoxides, hydroxyl radicals, and peroxides. We discuss using these biomarkers to predict risk of development and progression of DN, DR, and CVD, and to determine if they confer risk independently of the level of HbA1c. We also discuss methods and guidelines to document sample quality in such studies. These studies have the potential to validate unique biomarkers during the early stages of diabetes in those who are at high risk of diabetic complications. Information on basic mechanisms responsible for complications could also stimulate development of therapeutic approaches to delay or arrest them. The ultimate goal is to predict those requiring aggressive therapies during the earliest stages, when prevention or reversal of complications is still possible.