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The products of secondary xylem are of significant biological and commercial importance, and as a result, the biology of secondary growth and how intrinsic and extrinsic factors influence this process have been the subject of intense investigation. Studies into secondary xylem range in scale from the cellular to the forest stand level, with phenotypic analyses often involving the assessment of traits relating to cell morphology and cell wall chemical composition. While numerous techniques are currently available for phenotypic analyses of samples containing abundant amounts of secondary tissue, only a few of them (microanalytical techniques) are suitable when working with limiting amounts of secondary tissue or where a fine-scale resolution of morphological features or cell wall chemical composition is required. While polarised light microscopy, scanning electron microscopy, field emission-scanning electron microscopy and X-ray scattering and micro-tomography techniques serve as the most frequently used microanalytical techniques in morphotyping, techniques such as scanning ultraviolet microspectrophotometry, X-ray photoelectron spectroscopy, gas chromatography, Fourier-transform infrared spectroscopy and matrix-assisted laser desorption ionisation mass spectrometry serve as the most commonly used microanalytical techniques in chemotyping. Light microscopy, fluorescence microscopy, confocal laser scanning microscopy, transmission electron microscopy and Raman spectroscopy serve as dual micro morphotyping and chemotyping techniques. In this review, we summarise and discuss these techniques in the light of their applicability as microanalytical techniques to study secondary xylem.