Deep vein thrombosis is a serious complication of orthopaedic surgery and can lead to pulmonary embolism and long term post-thrombotic syndrome. A simulation model based on both epidemiological data and data from clinical trials was used to compare the long term cost effectiveness of standard prophylaxis with subcutaneous unfractionated heparin with that of desirudin (recombinant hirudin), in patients undergoing elective hip replacement. The analysis, which was performed before the price of desirudin was set, showed that prophylactic treatment with desirudin saved 4.5 life-years per 100 patients treated, compared with unfractionated heparin. Desirudin prophylaxis was dominant up to a total drug cost of 4400 Swedish kronor (SEK) per treatment. The results were robust against changes in the parameters used in several sensitivity analyses. This study showed that prophylactic therapy with desirudin compared with unfractionated heparin was more cost effective and potentially cost saving under a wide range of assumptions concerning the future price of desirudin in preventing deep vein thrombosis following elective hip surgery.