The clinical course of inflammatory bowel disease (IBD) is frequently associated with thromboembolic complications. The aim of this study was to investigate common thrombophilic markers in Turkish patients with active IBD. Twenty-seven consecutive patients with IBD who were followed-up at the Hacettepe University Hospital were recruited. All the patients were in the active disease state. International normalized ratio, activated partial thromboplastin time, lupus anticoagulant, anticardiolipin IgG, IgM antibodies, protein C, protein S, antithrombin-III, factor V, and factor II mutation of all the IBD patients and of a sex-matched and age-matched control group of non-IBD patients were measured. International normalized ratio, activated partial thromboplastin time, protein C, protein S, lupus anticoagulant, anticardiolipin IgG and IgM, and Proteins C and S mutations were comparable between the 2 groups, but antithrombin-III was significantly lower in the IBD group compared with healthy control group (P < 0.0001). As a conclusion, it is reasonable to assume that there may be a subpopulation of the patients with IBD, in whom thrombophilic abnormalities might be important for either disease manifestation or for thrombotic complications. Those hemostatic abnormalities could be either inherited or secondary to the ongoing disease process. Routine screening for the common markers of thrombophilia does not seem to be warranted unless simultaneous arterial and venous thrombosis, major organ thrombosis, strong family history of thrombophilia, unusual and recurrent thrombosis resistant to standard anticoagulant therapy are present. Further studies are definitely required to clarify these complicated associations.