Two methods were tested for calibration procedures of the 3-D coil system which is used as a source part of the magnetic tracker. Precise magnetometer's positions with respect to the coil system were used for determining of the nonorthogonality of the coil system as well as for determining of the magnetic moment. The needed number of the reference positions was measured to calculate six unknown calibrated parameters. In comparison, the 3-D coils system was also calibrated with a method which employs the orthogonal homogenous ac field generated in Helmholtz coils. The misalignment of up to two degrees was discovered.