Fourier transform infrared spectroscopy (FTIR) can provide crucial information on the molecular structure of organic and inorganic components and has been used extensively for chemical characterization of geological samples in the past few decades. In this paper, recent applications of FTIR in the geological sciences are reviewed. Particularly, its use in the characterization of geochemistry and thermal maturation of organic matter in coal and shale is addressed. These investigations demonstrate that the employment of high-resolution micro-FTIR imaging enables visualization and mapping of the distributions of organic matter and minerals on a micrometer scale in geological samples, and promotes an advanced understanding of heterogeneity of organic rich coal and shale. Additionally, micro-FTIR is particularly suitable for in situ, non-destructive characterization of minute microfossils, small fluid and melt inclusions within crystals, and volatiles in glasses and minerals. This technique can also assist in the chemotaxonomic classification of macrofossils such as plant fossils. These features, barely accessible with other analytical techniques, may provide fundamental information on paleoclimate, depositional environment, and the evolution of geological (e.g., volcanic and magmatic) systems.