A system and method for detecting and predicting low performing cells in a fuel cell stack. When the fuel cell stack is running and certain data validity criteria have been met, an algorithm collects the data, such as stack current density, average cell voltage and minimum cell voltage. This information is used to estimate predetermined parameters that define the stack polarization curve. The system defines a predetermined minimum current density that is used to identify a low performing cell. The system then calculates an average cell voltage and a minimum cell voltage at the minimum current density set-point, and calculates a cell voltage difference between the two. If the cell voltage difference is greater than a predetermined low voltage threshold and the minimum cell voltage is less than a predetermined high voltage threshold, the algorithm sets a flag identifying a potential for a low performing cell.