Chlorophyll fluorescence imaging provides a noninvasive, non-destructive method with which to measure heterogenous changes in photosynthetic metabolism in plants infected by pathogens. The availability of commercial imaging fluorimeters has helped make this technique available to the wider scientific community, but considerable care is needed, both in experimental design and in the interpretation of results, to make the most of this powerful analytical tool. The origins of changes in chlorophyll fluorescence yield are discussed and the use of conventional and novel combinatorial imaging approaches explored, together with complementary techniques such as thermal imaging. This review examines the use of chlorophyll fluorescence imaging as a method for the early detection of viral, bacterial and fungal infection, before symptoms are visible by eye, and also as a means with which to probe underlying pathogen-induced changes in host physiology in both compatible and incompatible interactions. The use of chlorophyll fluorescence imaging to study host physiology is greatly enhanced when the atmosphere around the leaf is manipulated and simultaneous measurements of gas exchange made: The cost to the host plant of different resistance mechanisms can be calculated, the fate of the products of photosynthetic electron transport determined and localised alterations in the source-sink status of host tissue visualised.