This paper presents a study on the topology-dependent magnet defect fault signatures in permanent-magnet motors. A new analytical approach is introduced to characterize the fault signatures in stator back electromotive force (EMF) and current waveforms using magnetic equivalent circuit. Stator winding configuration, winding connection type and location of damaged rotor magnets are some of the physical properties affecting the fault signature characteristics. Several cases with different number of pole and slot are investigated through the proposed method. In addition, different winding connections (including star and delta connection), different winding configurations (including single and double layer, fractional and full coil pitch), and different magnet defect number and location are scrutinized. It is shown that there are some cases exhibiting different fault patterns than the ones obtained through well-known fault models defined in the literature. It is essential to take these discrepancies into account in order to avoid false alarms. In addition, it is observed that some of the fault signatures show up in the stator back EMF spectrum but not in the current spectrum due to location and severity of magnet defect, and design specs. Comparative 2-D finite-element simulations and experimental results justify the theoretical magnet defect fault analysis and show the efficacy of the proposed approach.