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Hyperspectral imaging (HSI) in situ core scanning has emerged as a valuable and novel tool for rapid and non-destructive biogeochemical analysis of lake sediment cores. Variations in sediment composition can be assessed directly from fresh sediment surfaces at ultra-high-resolution (40–300 μm measurement resolution) based on spectral profiles of light reflected from sediments in visible, near infrared, and short-wave infrared wavelengths (400–2500 nm). Here, we review recent methodological developments in this new and growing field of research, as well as applications of this technique for paleoclimate and paleoenvironmental studies. Hyperspectral imaging of sediment cores has been demonstrated to effectively track variations in sedimentary pigments, organic matter, grain size, minerogenic components, and other sedimentary features. These biogeochemical variables record information about past climatic conditions, paleoproductivity, past hypolimnetic anoxia, aeolian input, volcanic eruptions, earthquake and flood frequencies, and other variables of environmental relevance. HSI has been applied to study seasonal and inter-annual environmental variability as recorded in individual varves (annually laminated sediments) or to study sedimentary records covering long glacial–interglacial time-scales (>10,000 years).