This paper presents a detailed study on topology dependent magnet defect fault signatures in permanent magnet (PM) motors. A new mathematical approach is introduced to analyze the fault signature behaviors in PM motors with different design specs such as combinations including winding types, number and location of stator coils / magnet defects etc. Thanks to the flexible features of the proposed method, it is possible to analyze various winding configurations (including full, short and fractional pitch, single and double layer, delta and star connection) and combination of multiple magnet defect effects on the motor variables' frequency spectrum. It is shown that depending on the motor topology, the corresponding spectrum can be different from others and the generalized fault models may not be valid. In addition, current or back-emf spectrums do not include any fault related harmonics in some cases or the fault components showing up in the stator back-emf do not show up in the stator current. Comparative 2-D Finite Element (FE) simulation and experimental results justify the theoretical magnet defect fault analysis and show the efficacy of proposed approach.