Heparin-induced thrombocytopenia (HIT) is a life-threatening complication in intensive care settings. The timely diagnosis and management of HIT are challenging, and the incidences of HIT and deep venous thrombosis (DVT) may be related to prophylactic anticoagulation standards in burn units. We therefore evaluated, using a questionnaire, prophylactic anticoagulation, HIT management, and incidences of DVT and HIT in burn centers located in the German-speaking part of Europe. In the 21 responding burn centers, 1611 patients were treated and the overall incidences for clinically overt DVT and HIT in 2008 were 1.1% and 1.4%, respectively. Burn centers using low molecular weight heparin (LMWH) subcutaneous for all patients had a low rate of DVT (0.9%) and significantly lower rates of HIT (0.2%) relative to all other centers (P < 0.05). The highest rates of HIT (2.7%) and DVT (3.8%) were found in burn centers administering unfractionated heparin intravenous. While current HIT guidelines do not specify the administration of unfractionated heparin or LMWH for burn patients, these data warrant controlled prospective studies to confirm the advantage of LMWH administration in burn patients.