A best evidence topic in cardiac surgery was written according to a structured protocol. The question addressed was whether the use of prophylactic postoperative low molecular weight heparin (LMWH) or unfractionated heparin after cardiac surgery would significantly reduce morbidity by reducing the incidence of deep vein thromboses (DVTs) and pulmonary emboli (PEs). Altogether 390 papers were identified on Medline. Relevant major guidelines were also searched together with their reference lists. Sixteen papers represented the best evidence on the topic. The author, journal, date and country of publication, patient group studied, study type, relevant outcomes, results and study weaknesses were tabulated. We conclude that the benefit of heparin prophylaxis for the prevention of DVTs and PEs is well established in non-cardiac surgery with reductions in the incidence of DVTs reported to be of the order of 50-70% in orthopaedic, general and obstetric surgery and in general medicine. No studies have yet been performed in cardiac surgery, but contrary to the view that DVTs are rare, in fact the incidence of DVT post-cardiac surgery is up to 15-20% and the incidence of PE is around 0.5 to 4% although many of these occur after discharge and many may be difficult to detect clinically. This is similar to the incidence of patients undergoing high risk general surgery. There is no evidence that heparin prophylaxis started the day after surgery increases the risk of pericardial effusions and the risk of bleeding complications is estimated to be 4%. Thus, we recommend that all patients post-cardiac surgery be commenced on heparin prophylaxis the day after their surgery and continue this up to discharge even if mobile. The particular regime should be guided by the ACCP recommendations for prophylaxis in high risk general surgical patients.