Auto-fluorescence emission of plant tissues can be a powerful reporter on plant biochemistry and physiology since it originates in substances inherent to primary or secondary metabolism. Plant bodies contain a plethora of intrinsic fluorescent compounds emitting practically all wavelengths of visible light. Moreover, the spectrum of fluorescent reporter signals was recently extended by a variety of fluorescent proteins that provide a new tool to mark whole cells or sub-cellular structures, study protein localization and monitor gene expression and molecule interactions. The imaging of such fluorescence signals reveals a possibility to acquire the information from as many as millions of points simultaneously, in vivo and in a non-invasive way thereby preserving integrity of cells and whole organisms. Imaging is particularly suited to visualize heterogeneity such as a localized immune response to invading pathogens. It can be applied both at macro- as well as micro-scales in two and three dimensions. The recent advancement in microscopy, the multi-photon microscopy, has made possible to monitor fluorescence signals, such as NAD(P)H fluorescence from intact leaf interior, that have been hidden to single-photon techniques.