A ship in a sea cruises with rolling, pitching, heaving etc because of environmental causes such as wind and wave. Those motions make crews or passengers feel inconvenience and they feel acceleration changes. Therefore, if lateral and vertical accelerations can be measured at a specific position in a ship, it can be known how discomfortable crews or passengers are. The motion monitoring system developed in this paper consists of measuring and communicating part including five accelerometers and gyro and a main computer which acquires measuring data and calculates motion indices. MSI(Motion Sickness Incidence) and MII(Motion Induced Interrupt) are calculated in real time using measured acceleration and angular rate. The validity of the developed system was confirmed through the real ship test of Hannara which is the school ship of Korea Maritime University.