Calibrated automated thrombin generation measurement in clotting plasma (endogenous thrombin potential, ETP) is being used increasingly to monitor the effects of anticoagulant drugs. Calibrated automated thrombography measures the concentration of thrombin in clotting plasma by monitoring the cleavage of a fluorogenic substrate (Z-Gly-Gly-Arg-7-amino-4-methylcoumarin) and comparing it with a constant known thrombin activity in a parallel nonclotting sample. This study compared the concentration-dependent effects of different factor IIa inhibitors on the ETP. In accordance with a theoretical prediction, the monovalent factor IIa inhibitors melagatran and argatroban reduced peak thrombin concentrations without a marked effect on the lag time of thrombin generation. However, both bivalent factor IIa inhibitors lepirudin and bivalirudin markedly prolonged the lag time of thrombin generation and thus behaved like “super” factor Xa inhibitors according to the theoretical model. These findings have important consequences for therapeutic drug monitoring using thrombin generation assays. For monitoring of hirudins, the lag time of thrombin generation seems to be a very sensitive parameter. In contrast, for monitoring of argatroban, the evaluation of the ETP seems to be useful.