The inertial/magnetic measurement units are an affordable instrument for the determination of orientation. The sensors embedded in the system are affected by nonidealities that can be greatly compensated by proper calibration, by determining sensor parameters, such as bias, misalignment, and sensitivity/gain. This paper presents an online calibration method for a three-axial magnetometer using a 3-D Helmholtz coil. The magnetometer is exposed to different directions of the magnetic field created by the 3-D coil. The parameters are estimated by using an unscented Kalman filter. The directions are calculated online by using a sensor parameter covariance matrix. The method evaluation is achieved by first running numerous simulations, followed by experiments using a real magnetometer, finally resulting in better accuracy of parameter estimation with a low number of measurement iterations compared with the method where magnetic field directions are determined manually.