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The activated clotting time is a bedside method routinely used to monitor heparin anticoagulation during operations requiring cardiopulmonary bypass. The thrombolytic assessment system heparin management test is a new bedside method for monitoring heparin effect. We compared these methods with respect to their ability to reflect the actual heparin concentration in plasma determined by an anti-FXa method.Two studies were done, an ex vivo study on ten patients who had coronary artery bypass using nonheparin-coated cardiopulmonary bypass circuits and full systemic heparinization and an in vitro study on single donor plasma spiked with heparin 0 to 10 IU/mL.Ex vivo study correlation coefficients of activated clotting time and the thrombolytic assessment system heparin management test clotting times versus anti-FXa-based heparin assay were low (r = 0.53, p = 0.002/r = 0.64, p < 0.001) in contrast with the corresponding correlation coefficients for the in vitro study (r = 0.98, p < 0.001/r = 0.99, p < 0.001). A substantial variability in duplicate activated clotting time determinations was noted, which was less pronounced with the thrombolytic assessment system heparin management test.The thrombolytic assessment system method does not correlate better to the actual amount of heparin during cardiopulmonary bypass procedures than the activated clotting time method, which should be performed in duplicate.