Disorders of fatty acid oxidation and of the carnitine cycle are an important cause of morbidity and mortality. With the introduction of expanded newborn screening, many of these conditions can be diagnosed and treated at birth, preventing several of the complications. Treatment of these conditions may include fasting-avoidance, diets low in fat containing specific fatty acids, and carnitine supplements. New types of therapies, nutritional and pharmacological, are being tested in humans and animal models of these conditions. Unfortunately, treatment is only partially effective for some conditions and we still do not understand completely the pathophysiology of end-organ damage caused by these inherited disorders.