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The ratio of the increments of flux linkages (RIFLs) of the primary-secondary, primary-tertiary and secondary-tertiary windings is the same as the corresponding turns ratio during normal operating conditions, magnetic inrush and over-excitation. The RIFL differs from the turns ratio during an internal fault. In this study, the authors propose an algorithm for protection, a faulted phase and winding identification for the three-winding transformer using the increments of flux linkages (IFLs). The IFLs of each pair of windings are estimated for a single-phase and a three-phase transformer with wye-connected windings. For a three-phase transformer with delta-connected windings, the differences of the IFLs are estimated to use the line currents because the delta winding currents are practically unavailable. In this study, six detectors are suggested for fault detection; three additional detectors and a rule for the faulted phase and winding identification are presented as well. The proposed algorithm can not only detect an internal fault, but also identify the faulted phase and winding of a three-winding transformer. The various test results with electromagnetic transients program (EMTP) generated data show that the proposed algorithm successfully discriminates the internal faults from normal operating conditions including magnetic inrush and over-excitation. This study concludes by implementing the proposed algorithm into a prototype relay based on a digital signal processor.