Hypertrophic cardiomyopathy(HCM) is a condition characterized by thickening of the heart muscle. This causes mid-systolic ventricular obstruction and/or left ventricular outflow tract obstruction, which can have an impact on the arterial waveform. The FloTrac/EV1000TM system is a non-invasive hemodynamic monitor that uses arterial pressure waveform analysis and is currently used for patients with cardiac compromise. However, little is known about the reliability of this system in HCM patients. A 19-year-old male patient who has been treated for HCM was scheduled for resection of the nerve of pterygoid canal for treatment of allergic rhinitis. Invasive arterial pressure monitoring that connected to the FloTrac/EV1000TM system was initiated. However, after induction of general anesthesia, the system started indicating very low cardiac index and even stopped measurement. All the other hemodynamic parameters seemed to be in the normal range. Here we describe the limitation of the FloTrac/EV1000TM system for an anesthetized patient with HCM.