The prevalence of hereditary thrombophilia is well known in patients with lower‐extremity thrombosis but only poorly studied in patients with thrombosis at unusual sites. Consequently, it is still unclear whether such patients should generally be screened for hereditary thrombophilia. We retrospectively analyzed 260 patients with thrombosis at unusual sites including thrombosis in portal, cerebral, retinal, and upper‐extremity veins with respect to the prevalence of FV Leiden, prothrombin G20210A, protein C, protein S, and antithrombin deficiency. In addition, all thrombotic episodes were analyzed for circumstantial risk factors. Used as controls, healthy volunteers (120) and patients with lower‐extremity thrombosis (292) showed overall prevalence of hereditary thrombophilia of 9.1% and 39.0%, respectively. The corresponding numbers were 33.3%, 34.3%, and 39.0% in patients with portal vein, upper‐extremity, and lower‐extremity thrombosis, respectively. In patients with cerebral vein thrombosis, however, the prevalence was significantly lower (23.5%). Patients with retinal vein occlusion did not show an increased frequency of thrombophilia at all (5.9%). In all five groups FV Leiden was by far the most frequent defect (4.4–27.1%), while prothrombin G20210A occurred rarer (2.5–7.6%). Protein C, protein S, and antithrombin deficiency were much less prevalent (0–3.1%) except for patients with portal vein thrombosis (4.8–7.1%). Compared to healthy individuals, the relative risk of thrombosis was 4.3 (2.2–8.1), 3.8 (1.8–7.7), 2.5 (1.0–6.1), 3.7 (1.5–8.6), and 0.6 (0.2–2.1) for patients with lower‐extremity, upper‐extremity, cerebral vein, portal vein, and retinal vein thrombosis, respectively. Circumstantial risk factors were more frequent in patients without than with hereditary thrombophilia and were found most often in patients with upper‐extremity thrombosis. In each group the most frequent circumstantial risk factor was different. However, oral contraceptives and cancer were found in all five groups. In conclusion, independent upon the presence of circumstantial risk factors, screening for hereditary thrombophilia is warranted in all patients with thrombosis at unusual sites except in those with retinal vein occlusion. Am. J. Hematol. 70:126–132, 2002. © 2002 Wiley‐Liss, Inc.