Spruce wood that had been degraded by brown-rot fungi (Gloeophyllum trabeum or Poria placenta) exhibiting mass losses up to 16% was investigated by transmission Fourier transform infrared (FT-IR) imaging microscopy. Here the first work on the application of FT-IR imaging microscopy and multivariate image analysis of fungal degraded wood is presented and the first report on the spatial distribution of polysaccharide degradation during incipient brown-rot of wood. Brown-rot starts to become significant in the outer cell wall regions (middle lamellae, primary cell walls, and the outer layer of the secondary cell wall S1). This pattern was detected even in a sample with non-detectable mass loss. Most significant during incipient decay was the cleavage of glycosidic bonds, i.e. depolymerisation of wood polysaccharides and the degradation of pectic substances. Accordingly, intramolecular hydrogen bonding within cellulose was reduced, while the presence of phenolic groups increased.