Fontan operation broke fresh ground in the treatment of patients with single ventricle anatomy by separating the systemic venous blood from pulmonary venous circulation. Survival rate following Fontan operation improved recently due to the discovery of patient specific factors, modifications in surgical techniques and improvement in postoperative patient care. Failure of Fontan circulation may happen in early or late follow-up period following Fontan operation. Progressive ventricular dysfunction, dysrhythmia, progressive hypoxemia, cyanosis, increase in pulmonary vascular resistance or protein-losing enteropathy may be observed in this patient group which is more frequently encountered at present. Conditions causing failure of Fontan circulation and the surgical or medical treatment options are discussed in this article.