The axial flow pump has been developed in Korea Artificial Organ Center. It consists of an impeller, a motor and a magnetic bearing. The magnetic bearing fully levitates the impeller not to contact with other parts of pump. However, in order to control the gap between the impeller and other parts, continuous gap sensing is necessary. The conventional gap sensors are relatively large to implant in artificial heart. Thus, the compact eddy current sensor system proper for artificial heart was developed and the performances were evaluated. It showed good results and has small size. However, the dependency of the sensor upon temperature and target material was shown also. Moreover, the output of sensor had nonlinear responses. These must be calibrated in further study.