Diet and nutrition have played an important role in maintaining physiological homeostasis. Recent literature emphasizes potential therapeutic effects of micronutrients found in natural products, indicating positive applications for controlling the pathogenesis of chronic diseases driven by an inflammatory nidus. Nutritional compounds which display anti-inflammatory and antioxidant effects have specific applications in preventing oxidative stress induced injury which characterizes their pathogenesis. Patient control over diet and disease has been demonstrated in diabetes mellitus, cardiovascular disease, rheumatology, carcinogenesis and other diseases. Polyphenolic compounds are ubiquitous dietary components, mainly flavonoids and tannins. Specific polyphenols are effective in scavenging reactive oxygen and reactive nitrogen species. They are able to modulate genes associated with metabolism, stress defence, drug metabolizing enzymes, detoxification and transporter proteins. Their overall effect is protective in overcoming damaging effects of chronic diseases and in delaying the degenerative effects of ageing. The mechanisms involved in radical scavenging activity are complex, determined by the structure of the compound, redox status of the environment and interactions with other agents. Atherogenic dyslipidaemia associated with a pro-inflammatory pro-thrombotic state in metabolic syndrome and related risk of fatty liver, arthritis, neurodegenerative disorders and certain types of cancers are ideal therapeutic targets for bioactive phytochemicals which can combat oxidative stress induced damage at a sub-cellular level. It is relevant that purified micronutrients isolated from natural products may be less effective than a combination seen in the natural product due to synergistic effects of interacting agents. Some of these mechanisms and potential therapeutic targets are discussed.