Anticoagulation in infants and children on a ventricular assist device presents particular challenges. Unfractionated heparin has poor bioavailability; it can be difficult to achieve a stable anticoagulant effect; and, in the long-term, there is a risk of osteopenia. Long-term warfarin can be difficult to manage in infants on formula milk with vitamin K supplementation. We review our recent experience with subcutaneous low molecular weight heparin. Two patients received a left ventricular assist device (Excor, Berlin Heart AG) as a bridge to transplantation. Initial anticoagulation consisted of unfractionated heparin infusion beginning 6 hours after implantation to maintain an activated partial thromboplastin time of 70 seconds, checked every 4 to 6 hours. Platelet count (aim >80,000/microl) and thromboelastography were assessed daily. Antithrombin required substitution to maintain levels >70 IU/dl. To optimize anticoagulation, both infants were switched to subcutaneous low molecular weight heparin twice daily aiming for an anti-Xa activity between 0.5 and 1.0 IU/ml. Aspirin was added on day 4, checking platelet aggregation every 2 to 4 days, aiming at arachidonic acid stimulated aggregation 10% to 30% of baseline, collagen 100% of baseline. Dipyridamole was added once stability was reached if platelets count exceeded 150,000/microl. There were no clinical thromboembolic or bleeding events. Both patients had successful transplantation.