Background Despite advances in pump technology, thromboembolic events/acute pump thrombosis remain potentially life-threatening complications in patients with continuous-flow left ventricular assist devices (CF-LVAD). We sought to determine early signs of thromboembolic event/pump thrombosis in patients with CF-LVAD, which could lead to earlier intervention. Methods We analysed all HeartMate II recipients (n = 40) in our centre between December 2006 and July 2013. Thromboembolic event/pump thrombosis was defined as a transient ischaemic attack (TIA), ischaemic cerebrovascular accident (CVA), or pump thrombosis. Results During median LVAD support of 336 days [IQR: 182-808], 8 (20 %) patients developed a thromboembolic event/pump thrombosis (six TIA/CVA, two pump thromboses). At the time of the thromboembolic event/pump thrombosis, significantly higher pump power was seen compared with the no-thrombosis group (8.2 +/- 3.0 vs. 6.4 +/- 1.4 W, p = 0.02), as well as a trend towards a lower pulse index (4.1 +/- 1.5 vs. 5.0 +/- 1.0, p = 0.05) and a trend towards higher pump flow (5.7 +/- 1.0 vs. 4.9 +/- 1.9 L m, p = 0.06). The thrombosis group had a more than fourfold higher lactate dehydrogenase (LDH) median 1548 [IQR: 754-2379] vs. 363 [IQR: 325-443] U/L, p = 0.0001). Bacterial (n = 4) or viral (n = 1) infection was present in 5 out of 8 patients. LDH > 735 U/L predicted thromboembolic events/pump thrombosis with a positive predictive value of 88 %. Conclusions In patients with a CF-LVAD (HeartMate II), thromboembolic events and/or pump thrombosis are associated with symptoms and signs of acute haemolysis as manifested by a high LDH, elevated pump power and decreased pulse index, especially in the context of an infection.