An increased interest in the antioxidant effects of medicinal plants has developed in recent years. Identifying antioxidant compounds present in medicinal plants and elucidating the mechanism by which they prevent oxidation have been the focus of the research community. We performed a systematic and exhaustive review aimed at analyzing the available data regarding the beneficial effects of secondary metabolites in plants. The result of this review is presented as a description of free radicals, as well as cellular and physiological oxidative stress, is provided. The origin and source of antioxidant compounds, and the cellular and molecular mechanism by which they exert antioxidant effects, have been reported. The absorption, distribution and, elimination of antioxidants are mentioned. The beneficial effects of secondary metabolites of medicinal plants in various high incidence disease conditions were also reviewed. Finally, disease states that benefit from antioxidant compounds includes diabetes, cancer, cardiovascular diseases, and liver, brain and, intestinal diseases.