The present study was undertaken to identify chlorophyll fluorescence (CF) parameters that can quantify changes in PSII associated with plant responses in three different wheat pathosystems of foliar, stem-base and ear diseases. The pathosystems included powdery mildew caused by Blumeria graminis, eyespot caused by Oculimacula yallundae or Oculimacula acuformis and Fusarium head blight (FHB) caused by Fusarium culmorum, F. avenaceum or F. langsethiae. Fast CF transients (OJIP) were analysed with the JIP-test to determine changes in PSII photochemistry. Measurements on asymptomatic leaves showed that electron transport related parameters (ETo/RC, ψo and ϕEo) were important to identify varietal differences in resistance to powdery mildew during early stages of infection. The same parameters also allowed differentiation between F. langsethiae and other Fusarium spp. Where infections were caused by the necrotrophic pathogens, Oculimacula spp., F. culmorum or F. avenaceum, changes related to maximum efficiency of PSII photochemistry (Fv'/Fm') as well as flux of dissipated (DIo/RC), trapped (TRo/RC), or absorbed (ABS/RC) energy per active reaction centers were significant in detecting biotic stress and the effectiveness of fungicide treatment for disease control. Our results demonstrated that Fv'/Fm' correlated significantly with visual disease and pathogen DNA of different wheat pathosystems. OJIP was shown as a sensitive technique that can be explored as diagnostic tool in future crop disease management and varietal breeding programs.