The cost reduction and the improvement of a life performance are necessary for the dissemination of Polymer Electrolyte Fuel Cell (PEFC). If the degradation of the fuel cell was able to be diagnosed at the early stage, the life performance can be improved by applying appropriate processing to PEFC. We have been proposing the PEFC Performance Diagnose System (PPDS) which diagnoses the state of each polarization (the resistance polarization, the activation polarization and the diffusion polarization) by analyzing transient response with Turuga Electric Corporation since 2002. Since 2014, the application of our PPDS to a PEFC short stack was tried because it was able to diagnose each degradation factor of a PEFC single cell. As a result, the PPDS not only found out a degradation cell in the four cells short stack but also was able to diagnose the degradation factor of this deteriorated cell. Therefore, this paper aims to grasp the correlation between the degradation factor and the cell position of the PEFC Short Stack using our PPDS, and the PPDS was able to find the unit with the deteriorated cell when it diagnoses each unit composed of four cells in the stack. As a result, because we elucidated the correlation between the degradation factor and the cell position of a stack, we can propose the structure of a PEFC stack where deteriorating is not caused easily. Moreover, we can apply our PPDS as a maintenance device for a fuel cell vehicle and a domestic use fuel cell.