Analyzed by a quantitative method based on diffuse reflectance infrared Fourier transform spectroscopy, pectins extracted from different regions (outer skin, peel, and waste) of citrus fruits (red orange, lemon, and grapefruit) via microwave-assisted hydrodiffusion show significant variations. All polymers obtained are low-methoxyl pectins, with high contents in galacturonic acid regions. The degree of esterification (DE) of pectin extracted from different regions increases in the order waste < peel < outer skin for red orange, inverting for lemon. Thus, the pectins with the lowest DE are those extracted from red orange waste and lemon outer skin (∼25%). These findings open the route to nutraceutical- and pharmaceutical-grade pectins from citrus, in which the source fruit and its regions may be chosen, according to the desired DE.