Approximately 10% of patients with mechanical ventilation experience prolonged weaning and also have an increased morbidity and mortality. Once spontaneous breathing trials have failed the organ systems responsible should be identified. This can be accomplished during the spontaneous breathing trial using clinical examination, measurement of blood gases, echocardiography and imaging techniques. Specific patterns allow the diagnosis of pathological respiratory mechanisms, weak ventilatory muscles, heart failure, myocardial ischemia and psychiatric problems. Respiratory and cardiac limitations of weaning can be overcome by reducing the ventilatory load, training of the ventilatory muscles and reducing cardiac workload. A cooperative sedation strategy as well as an early start of weaning and rehabilitation can prevent prolonged weaning in critically ill patients.