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This paper proposed a semi-analytical method for calculating eddy-currents losses in an inner-rotor type axial flux permanent magnet machine (AFPM), which have surface-mounted PM rotor structure and inserted PM rotor structure. The fractional slot concentrated winding has large amount of magneto-motive force (MMF) harmonics, which induce extra eddy-current losses in rotor. In the proposed method, each MMF harmonic is applied to a simplified finite element analysis model which is treated as time-harmonic magnetic problem, and the losses of each order are superposed. Various fractional slot winding designs are studied when equipped two different rotor structures.