Defects within the interatrial septum (IAS) can be a source of significant right-to-left shunting and hypoxemia, particularly after placement of a left ventricular assist device (LVAD). We report a case of LVAD placement in which an unrecognized IAS tear occurred intraoperatively, leading to profound arterial desaturation. Transesophageal echocardiography (TEE) was instrumental in making the diagnosis. Certain intraoperative events increased the pressure gradient between the right and left atria, aggravating hypoxemia. We recommend that patients undergoing LVAD placement be screened intraoperatively with TEE for unrecognized IAS defects. Re-examination of the IAS should occur on weaning from cardiopulmonary bypass.