Heparin-induced thrombocytopenia is a severe drug adverse effect with possible dramatic consequences. The risk is 0.1% to 5%. The costs of heparin-induced thrombocytopenia in France were estimated using the Programme Médicalisé des Systèmes d'Information (PMSI) national discharge database. Hospitalizations with heparin-induced thrombocytopenia were identified using diagnostic codes. Costs were assessed from the perspective of the French Sickness Fund or hospitals. Heparin-induced thrombocytopenia could be the reason of admission or could occur during the stay and lead to a different tariff or to additional costs associated with extra length of stay. Direct costs were also estimated from experts' opinions. A sensitivity analysis was performed from data collected in 1 center. During 2005, 445 hospitalizations with heparin-induced thrombocytopenia codes were identified. For 45 patients, the main diagnosis was heparin-induced thrombocytopenia; for the remaining 400 patients, heparin-induced thrombocytopenia occurred during the hospital stay. Tariffs and extra costs were used to estimate an overall average cost of 3230 for heparin-induced thrombocytopenia. For patients with heparin-induced thrombocytopenia as main diagnosis, the average cost was 3400; for the patients with heparin-induced thrombocytopenia that occurred during the stay, 1910 was due to an increased of the tariff and 3348 to an increased length of stay. Estimated direct costs of an episode were 3350 to 3700. Different methods were used to arrive at an estimated cost of 3500 for a heparin-induced thrombocytopenia episode for inpatients. One limitation of the study is that heparin-induced thrombocytopenia tends to be underreported by physicians during hospitalization.