The recently reported reductions in the incidence of post-operative venous thromboembolism (VTE) are related to the widespread use of prophylactic anticoagulants. Many uncertainties remain with regard to the most effective ways to use thromboprophylaxis, however. The trend towards shorter hospital stays means that patients may receive less than the recommended 7–10 days of prophylaxis. Prolonged periods of thromboprophylaxis may be beneficial for patients at high risk of post-operative VTE, such as those undergoing major orthopaedic surgery. The relative rarity of symptomatic deep vein thrombosis and pulmonary embolism means that very large patient populations are required for studies that rely on clinical endpoints, but studies using venographic endpoints have shown 28–35 days of prophylaxis with low-molecular-weight heparin to be more effective than 10–14 days. Other factors that may influence the efficacy of thromboprophylaxis include the timing of the first injection and the choice of agent.