A system and method for balancing the states of charge between a plurality of energy storage modules in a hybrid vehicle is disclosed. The method comprises determining states of charge of individual energy storage modules in said plurality of energy storage modules operatively connected to a power source in the hybrid electric vehicle. The vehicle is operated using a subset of the plurality of energy storage modules when the states of charge of said subset the plurality of energy storage modules is outside of a tolerances relative to the remaining energy storage modules of said plurality of said energy storage modules. The energy storage modules may be charged or discharged using the method in order to equalize the states of charge of the energy storage modules.