Philosophiae Doctor - PhD / Proton exchange membrane fuel cells (PEMFC) converts chemical energy from the electrochemical reaction of oxygen and hydrogen into electrical while emitting heat, oxygen depleted air (ODA) and water as by-products. The by-products have useful functions in aircrafts, such as heat that can be used for ice prevention, deoxygenated air for fire retardation and drinkable water for use on board. Consequently, the PEMFC is also studied to optimize recovery of the useful products. Despite the progress made, durability and reliability remain key challenges to the fuel cell technology. One of the reasons for this is the limited understanding of PEMFC behaviour in the aeronautic environment. The aim of this thesis was to define a comprehensive non-intrusive diagnostic technique that provides real time diagnostics on the PEMFC State of Health (SoH). The framework of the study involved determining factors that have direct influence on fuel cell life in aeronautic environment through a literature survey, examining the effects of the factors by subjecting the PEMFC to simulated conditions, establishing measurable parameters reflective of the factors and defining the diagnostic tool based on literature review and this thesis finding.