We review the muscular dystrophies and metabolic myopathies associated with myalgia and rhabdomyolysis together with some less well-recognized associations based upon the personal practice of the authors. A careful history and clinical examination will direct investigation towards an accurate molecular diagnosis. Non-specific exercise-induced myalgia in the presence of muscle hypertrophy and a high creatine kinase will point towards a muscular dystrophy. Symptoms occurring within minutes of exercise and with isometric contraction, especially with a history of a 'second wind' phenomenon, suggest a disorder of glycogen metabolism. In those patients in whom symptoms occur after prolonged exercise, infections, fasting, stress, and cold, a disorder of fatty acid oxidation should be considered. Heat-induced rhabdomyolysis caused by exercising in hot and humid climates should lead the clinician to suspect a mutation in RYR1. Serum creatine kinase level should be a checked in all children presenting with leg pains. A careful history and examination and laboratory confirmation of myoglobinuria will target investigations leading to a correct molecular diagnosis.