A 58-year-old woman was referred to our department with subacute onset dyspnea on effort. A transthoracic echocardiogram revealed mobile left atrial mass originating from the intra-atrial septum, and almost obstructing the left atrial outflow in diastole. From continuous doppler recordings of the tricuspid valve, a systolic pulmonary artery pressure of 114mmHg was estimated. The tumor was exposed through a left atriotomy after bicaval cannulation for cardiopulmonary bypass (CPB). We performed complete excision of the tumor with the endocardium of the intra-atrial septum, to which it was attached. The defect was closed directly with running sutures. The CPB was weaned off uneventfully, however, there was moderate mitral regurgitation shown by transesophageal echocardiogram. Repeat cardioplegic arrest was induced and the mitral valve was exposed again, and mitral valvoplasty was performed. The mitral incompetence was probably due to an extreme tension of the mitral annulus after closure of the resulting intra-atrial defect.