This paper addresses technical challenges encountered in calibrating digital-output (DO) MEMS vibration sensors (accelerometers and gyroscopes). The first challenge comes from the traceability of measurements of DO vibration sensors. While the primary and comparison cal-ibration methods of analog-output vibration pickups are well established, no international standard for calibration of DO vibration sensors exists in ISO or IEC. A new calibration sys-tem developed in KRISS for digital-output MEMS accelerometers is introduced. It does not only provide a systematic way of realizing real-time communication with DO MEMS accel-erometers but also to fulfil requisites for the legacy vibration calibration system. A high-speed serial communication prototype for DO accelerometers is shown to be successful for real-time vibration measurement. The traceability of vibration measurement and calibration of digital-output accelerometers is shown to be not feasible without the real-time communication mod-ule properly integrated to the legacy calibration system. Furthermore, this paper unfolds un-expected observations from the DO MEMS accelerometers under calibration, which are never observed from the analogue-output accelerometers. The first one was it that the measured vi-bration frequency from DO MEMS accelerometers was not identical to that of the analog ref-erence accelerometer. It is shown to cause serious amplitude distortion and phase shift of measured vibration signals from the DO accelerometers. A mathematical model is proposed to consider those distortion effects. A simple resampling scheme is shown to enable the distor-tion-free amplitude and phase estimation for the simple harmonic vibration calibration signals. Another useful and realistic approach to the distortion-free amplitude and phase estimation for DO MEMS accelerometers and gyroscopes, referred to the "use of external sampling clock", is also presented with much emphasis. Its performance and significance are compared to those of the proposed resampling method.