P>Fourier-transform infrared (FT-IR) spectroscopy combined with microscopy enables chemical information to be acquired from native plant cell walls with high spatial resolution. Combined with a 64 x 64 focal plane array (FPA) detector, 4096 spectra can be simultaneously obtained from a 0.3 x 0.3 mm image; each spectrum represents a compositional and structural 'fingerprint' of all cell wall components. For optimal use and analysis of such a large amount of information, multivariate approaches are preferred. Here, FT-IR microspectroscopy with FPA detection is combined with orthogonal projections to latent structures discriminant analysis (OPLS-DA). This allows for: (i) the extraction of spectra from single cell types, (ii) identification and characterization of different chemotypes using the full spectral information, and (iii) further visualization of the pattern of identified chemotypes by multivariate imaging. As proof of concept, the chemotypes of Populus tremula xylem cell types are described. The approach revealed unknown features about chemical plasticity and patterns of lignin composition in wood fibers that would have remained hidden in the dataset with traditional data analysis. The applicability of the method to Arabidopsis xylem and its usefulness in mutant chemotyping is also demonstrated. The methodological approach is not limited to xylem tissues but can be applied to any plant organ/tissue also using other techniques such as Raman and UV microspectroscopy.