Asplenia syndrome (AS) is a complex disorder that includes a variety of cardiovascular and gastrointestinal malformations (GMs), and its prognosis remains poor. We treated 40 AS patients between 2000 and 2010, 10 of whom underwent surgery to correct GMs. These comprised 7 hiatus hernias (HH), 1 intestinal malrotation (IM), 1 stomach volvulus, and 1 ompalocele. In this review, we consider the optimal surgical timing and methods of management, especially for HH and IM. Surgery was performed in 6 of 7 HH patients. Four of those underwent laparotomy, 1 thoracotomy, and 1 laparoscopy. The Toupet method or fixation of the His angle or hiatus closure was selected in each case. Because the stomach intruding into the mediastinum may cause pulmonary venous obstruction and respiratory impairment, surgical repair is preferably performed prior to Glenn surgery. Among the 9 IMs, 8 were nonrotational and required no treatment, and only 1 required surgical treatment. GMs in AS are difficult to manage because of the unique anatomy, meaning there are no fixed surgical techniques. Each patient must be carefully examined preoperatively, and the optimum surgical method selected. Close collaboration with cardiovascular surgeons is vital when determining the timing and method of surgery.