Health monitoring systems are used to assess building damage immediately after an earthquake and have become widely utilized in Japan. For example, the system developed by the authors has been installed in more than 60 buildings since 2014. Such systems mostly rely on accelerometers to estimate the building performance. Recently, Micro electro mechanical system (MEMS) accelerometers have been increasingly applied for such uses due to their economic advantages. However, MEMS accelerometers are known to have relatively low measurement accuracy for certain frequency band excitations compared to servo type accelerometers. Past research has been undertaken to test their measurement accuracy, however, few studies review their performance under long period and large amplitude seismic motions. Evaluation of measurement accuracy in such conditions is essential since the system is also installed in tall buildings and isolated buildings with relatively long natural periods. Therefore, this study evaluates the measurement accuracy of the MEMS accelerometer under long period and large amplitude vibration based on the results of shake table testing.