Objective: To compare economic impacts of anti-thromboembolism prophylaxis with two medications – new pentasaccharide fondaparinux versus low molecular weight heparin (LMWH) – in major orthopaedic surgery, such as hip and knee replacement and hip fracture repair, in Switzerland. In order to meet this objective, three parameters were determined for an observation period of 5 years. (1) Outcomes: Frequency of deep vein thrombosis (DVT), pulmonary embolism (PE) and their complications. (2) Cost burden of disease: Determination of the costs of DVT, PE and complications not prevented despite prophylaxis. (3) Total costs of prophylaxis: Costs were calculated from the perspective of the health insurance scheme. Methods: In order to determine outcomes and cost burden of disease, a model was applied which generates the post-surgery course of thromboembolic events (TE) and their complications for individual cohorts of patients undergoing hip and knee replacement surgery and hip fracture repair. These findings were allocated to the Swiss standard diagnostic and therapeutic measures (resource consumption), which enabled subsequent calculation of the costs of TE, including complications not prevented in spite of prophylaxis (cost burden of disease) based on standard Swiss tariffs. Additionally, total costs of prophylaxis, including costs of medications and monitoring, were determined. Results: In Switzerland, the following outcomes (expressed as percentage of the number of patients undergoing surgery) can be expected for TE prophylaxis with LMWH and with fondaparinux: DVT 3.4 vs. 2.3%, PE 1.4 vs. 0.7%, recurrent DVT 0.2 vs. 0.1%, post-thrombotic syndrome 4.8 vs. 3.5%. The costs of non-prevented TE and their complications add up to CHF 437 vs. CHF 306 per patient undergoing major orthopaedic surgery; the total cost burden for Switzerland amounts to CHF 13.4 million vs. CHF 9.4 million (30% less). Thus, despite higher medication costs, the use of fondaparinux instead of LMWH saves a total of CHF 105 per operated patient from the perspective of the health insurer. Conclusion: Fondaparinux is superior to LMWH in regards to both clinical efficacy and financial costs. This statement is confirmed by sensitivity analysis with different parameters over a broad range.