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Estimating the position of the bucket or tool on an agricultural/construction vehicle is becoming increasingly important to enable operator assistance such as automation of repetitive movements. Such end-effector position estimation is normally done through measurement of individual actuator’s movements inside kinematic linkage mechanisms that move the end-effectors. This paper develops an alternate inertial measurement unit (IMU) based end-effector position estimation system that offers significant advantages of low cost and easy installation. An IMU located on a rotating linkage in a mechanism is used to estimate the angular motion of the linkage. Key challenges arise from the fact that the accelerometer signals of the IMU experience significant disturbances from dynamic accelerations and from vehicle and terrain-induced vibrations. First, an adaptive feedforward algorithm is used to remove the influence of vibrations on the accelerometer signals. Then a nonlinear observer is utilized to combine accelerometer and gyroscope signals and reject the influence of vehicle accelerations. Experimental results are presented from a laboratory test rig and preliminary experimental results from a full-scale tracked skid steer loader vehicle. The results show that an accuracy better than 1 degree in linkage orientation estimation is achieved in the presence of vibration disturbances.