This paper is focused on development of models for measuring lateral and vertical track irregularities from corresponding accelerometers of an in-service high-speed train. Generally, the track irregularity was measured by a special railway inspection vehicle or system with contact or non-contact sensors. However, the sensors are very expensive and vulnerable to a harsh environment. Displacement estimation from an inertial measurement unit and its wave-band filtering was already developed in the previous study, and it was found that their results included not only the track irregularities but also other information such as phase delay of the applied filters, and suspension and conicity of the wheel. To identify the track irregularities from those results, a compensation filtering method was proposed. Each directional compensation filter was derived by using a system identification method with the estimated directional displacement as input and the corresponding track irregularities as output. In this paper, they are integrated into a model for each direction and applied to the measured lateral and vertical acceleration data from the axle-box and bogie of an in-service high-speed train. Their results are compared with the data from the track geometry measurement system. From the comparison, the proposed models are a useful tool for the measurement of the track irregularities using accelerometers of in-service high-speed trains.