Introduction There is a worldwide trend towards a more liberal use of ventricular assist devices (VADs) as a definitive treatment for patients in end-stage heart failure. This has also led to a new set of complications related to the prolonged interaction between the native heart and the device. Methods We report a case of, late, de novo aortic regurgitation (AR), leading to acute pulmonary edema in a 56-year-old man, 20 months after the implantation of a left ventricular assist device (LVAD), the Jarvik 2000 Flowmaker®, as destination therapy for end-stage heart failure. Results The Jarvik 2000 was working well at check up at level 3 of assistance, i.e. generating a flow between 3–5 l/min at 10,000 rpm. The only new finding was a moderate, de novo, AR at trans-thoracic echocardiogram (TTE). The patient was assisted in intensive care with inotropic and diuretic support and made a good recovery. He remains under close follow up in NYHA class II with the same level of mechanical assistance and a more intensive diuretic therapy. Conclusions This case shows how dramatic the onset of de novo AR in patients with LVAD can be. The AR occurred despite the presence of the ILS (intermittent low speed) that allows the opening of the native aortic valve for 8 seconds every 64 and should, theoretically, preserve the native aortic valve. To our knowledge, this is the first report of de novo AR in a patient with the Jarvik 2000 axial flow device.