Described is a method and system for reducing system penalty from polarization mode dispersion. The method includes receiving a plurality of signals at a receiving end of a transmission line, each signal being received on one of a plurality of channels of the transmission line and measuring a signal degradation of at least one of the channels of the transmission line. An amount of adjustment of a polarization controller is determined based on the signal degradation, the amount of adjustment being selected to reduce the polarization mode dispersion. The amount of adjustment is then transmitted to the polarization controller.