Cortriatriatum is a rare congenital cardiac disorder with fibromuscular band (diaphragm) dividing the left atrium (LA) into the proximal and distal parts. Surgical correction of cortriatriatum requires full preoperative evaluation of the structural anomalies including the LA diaphragm and their pathophysiology. In the present case, a 44 year-old lady diagnosed as cortriatriatum underwent surgical correction. Intraoperative three-dimensional transesophageal echocardiography provided detailed information regarding the shape and extent of the LA diaphragm, which had been partially evaluated by preoperative two-dimensional transthoracic and transesophageal echocardiography, and facilitated the intraoperative patient management and surgical decision making.