Four gas Diffusion Layer (GDL) materials have been investigated. Each Membrane Electrode Assembly (MEA) was manufactured with identical catalyst and binder loadings. MEAs were tested in-situ using a ‘Fuel Cell Component Analyser’ and polarisation curves produced and compared. GDL properties obtained in a previous work were considered for the analysis of the results. Results show differences in the polarisation response for different GDL structures; indicating changes in resistance loss, mass transport loss, and the flooding effects on fuel cells due to GDL structure.