Currently, modern chronic diseases are the leading killers in Westernised society and are increasing rampantly in developing nations. Considerable knowledge has accumulated in recent decades showing that physical exercise can be a very effective non-pharmacological strategy in the treatment of these pathologies, and as a result, several types of physical exercise are recommended in this matter. Aerobic exercise has been recognised as a safe and beneficial physical training modality for a number of chronic conditions, yet physicians do not know how to prescribe it. This chapter aims to discuss the effects of aerobic exercise in the treatment of metabolic syndrome-related disorders (diabetes, hypertension and obesity), heart and pulmonary diseases (coronary heart disease, chronic obstructive pulmonary disease and asthma), locomotive apparatus disorders (rheumatoid arthritis, osteoporosis systemic lupus erythematosus and fibromyalgia), neurological diseases (multiple sclerosis), and gastrointestinal disorders (Crohns Disease). The suggested potential mechanisms for the beneficial effects of aerobic exercise are discussed and some basic guidelines for exercise prescription in this kind of populations are given.