This paper explores and theoretically reports the effects of different magnet structures on the cogging torque and the total harmonic distortion of the output waveforms from a permanent magnet generator. The generator is a radial flux machine and four different structures are considered for the magnet arrangement in the rotor component and modelled in the Ansys/Maxwell electromagnetic simulation program. This three-phase machine exhibits different behaviours towards various magnet structures, i.e. rectangular, inclined slotted rectangular, skewed double rectangular and inclined slotted skewed double rectangular, respectively. It has been proven by finite element analysis and Fourier analysis that both the cogging and total harmonic distortion values vary significantly for all models. The cogging torque values change in the range of 89.95 to 436.75 mNm and the lowest cogging torque is measured for the inclined slotted skewed double rectangular magnet geometry, while the conventional rectangular magnet geometry yields the worst value with 436.75 mNm. Furthermore, the total harmonic distortion values varies between 1.63 and 3.55 for different magnetic orientations. While the worst total harmonic distortion value is obtained from the inclined slotted rectangular magnet, the best total harmonic distortion is acquired from the skewed double rectangular magnet. All these results will provide scientists and engineers with important information in order to obtain more efficient machines.