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This paper is concerned with orientation estimation using inertial and magnetic sensors. A quaternion-based indirect Kalman filter structure is used. The magnetic sensor output is only used for yaw angle estimation using two-step measurement updates. External acceleration is estimated from the residual of the filter and compensated by increasing the measurement noise covariance. Using the direction information of external information, the proposed method prevents unnecessarily increasing the measurement noise covariance corresponding to the accelerometer output, which is not affected by external acceleration. Through numerical examples, the proposed method is verified.