OBJECTIVES: The purpose was to conduct a cost-effectiveness analysis (CEA) of enoxaparin versus fondaparinux in the treatment of deep-vein thrombosis (DVT) in Poland. METHODS: Data concerning efficacy and safety of compared therapies were taken from the clinical-effectiveness analysis which was based on the systematic literature review. Due to lack of statistically significant differences in comparison of enoxaparin versus fondaparinux, economic profitability estimation was performed as a cost-minimisation analysis. Decision model was created by using MS Excel. Total costs of analysed therapies were estimated from the perspective of both payers in Poland (National Health Fund and patient). The minimisation analysis involved comparison of treatment with enoxaparin (1 mg/kg body mass, twice daily) versus fondaparinux (5; 7,5 or 10 mg – depending on the patient's body mass, once daily). The time horizon of the analysis was 3 months (consistent with clinical trials). It was assumed that efficiency of interventions in that period of observation was constant. The costs were not discounted. The stability of obtained results was checked in one-way and two-way sensitivity analysis through change of key parameters and assumptions of the model. RESULTS: The results of the cost-minimisation analysis are as following: treatment of one patient using enoxaparin in the 3 month time horizon is 312.50 PLN cheaper than fondaparinux therapy. Clinical effects of assessed treatment strategies are comparable, based on the data from randomised clinical trials. One-way and two-way sensitivity analysis proved that therapy with enoxaparin is a less costly than with fondaparinux in the treatment of deep-vein thrombosis for most parameters taken into account in the sensitivity analysis. CONCLUSIONS: Treatment of deep-vein thrombosis using enoxaparin is a less expensive option in comparison with fondaparinux from both payers’ perspective (National Health Fund and patient) in Poland.