A 74-year-old woman presented with progressive dyspnea on exertion. Transthoracic echocardiography (TTE) demonstrated significant left ventricular outflow tract (LVOT) obstruction with a pressure gradient of 100 mmHg caused by a sigmoid septum (SS). Mitral regurgitation (MR) of a mild to moderate degree occurred due to systolic anterior motion (SAM) of the anterior mitral leaflet (AML), with no intrinsic mitral valve (MV) abnormality. Myectomy of the hypertrophied septal bulge ameliorated the pressure gradient to 8 mmHg with similar MR. However, just before the sternal closure, hemodynamic status deteriorated drastically to ventricular fibrillation. MR exacerbated to a severe degree with an uncertain etiology; thus, a mechanical prosthetic valve was implanted. The postoperative course was complicated by prolonged mechanical ventilation due to massive pulmonary edema and complete atrioventricular block (CAVB) requiring permanent pacemaker implantation. One year postoperatively, the patient is asymptomatic and TTE revealed no residual pressure gradient with an iatrogenic ventricular septal defect (VSD). This case, the first published surgical experience of SS, may indicate that secondary MR, which is usually relieved by sufficient myectomy in hypertrophic cardiomyopathy (HCM), can exacerbate markedly, and that myectomy might not be advisable in SS. The therapeutic strategy must be considered carefully before embarking on surgical intervention.