The worldwide annual incidence of venous thrombosis is estimated at 1 in 1000 individuals, and associated pulmonary embolism represents a major cause of morbidity and mortality. Thrombophilia may be an inherited or acquired condition, with the former identified in approximately 25-30% of patients with thromboembolic disease. Recently published guidelines on thrombophilia testing recommend assays for protein C, protein S and antithrombin; a modified activated protein C resistance test (with factor V-deficient plasma); polymerase chain reaction for prothrombin G20201A, together with prothrombin time, activated partial thromboplastin time, thrombin clotting time and assays to detect antiphospholipid antibodies. This review highlights some of the issues that laboratories should consider when employing tests for the diagnosis of thrombophilia.