A system and method for providing component and sub-system state of health prognosis in a complex system using fault models and component aging models. The method includes determining a current state of health value for a sub-system using fault signature test results and determining current state of health values for a plurality of components in the sub-system using the fault signature test results. The method also determines current state of health values for components in the system that cannot use fault signature test results using a first probability model and the current state of health values for the plurality of components. The method determines predicted future state of health values for the components in the sub-system using component aging models and determines a predicted future state of health value for the sub-system using a second probability model and the future state of health values of the components.