Systems and methods for health monitoring of complex systems are disclosed. In one embodiment, a method includes receiving a plurality of signals indicative of observation states of plurality of operating variables, performing a combined probability analysis of the plurality of signals using a diagnostic model of a monitored system to provide a health prognosis of the monitored system, and providing an indication of the health prognosis of the monitored system. In some embodiments, the monitored system may be an onboard system of an aircraft.