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Changes in the volume covered by mucin-secreting goblet cell regions within colon thin sections may serve as a mean to differentiate between ulcerative colitis and infectious colitis. Here we show that the rapid, quantum cascade laser-based mid-infrared microspectroscopy might be able to contribute to the differential diagnosis of colitis ulcerosa, an inflammatory bowel disease. Infrared hyperspectral images of mouse colon thin sections are obtained within 7.5 minutes per section with a pixel size of 3.65 x 3.65 µm² and a field of view of 2.8 x 3.1 mm². The spectra are processed by training a random decision forest classifier on the basis of k-means clustering on one thin section. The trained algorithm was then applied to 5 further thin sections for a blinded validation and it was able to identify the goblet cells in all sections. The rapid identification of goblet cells within these unstained, paraffinized thin sections of colon tissue is enabled by the high content of glycopeptides within the goblet cells as revealed by the pronounced spectral signatures in the 7.6 µm – 8.6 µm and the 9.2 µm – 9.7 µm wavelength ranges of the electromagnetic spectrum. Even more so, the simple calculation of the ratio between the absorbance values at 9.29 µm and 8.47 µm provides the potential to further shorten the time for measurement and analysis of a thin section down to well below 1 minute.