The large glycosylated domains obtained from the rat intestinal mucin Muc2 were isolated from the large and small intestine of the inbred rat strains GOT-W and GOT-BW. The expression of the rat Muc2 in the large intestine was confirmed immunochemically and by Northern blotting. Released oligosaccharides were structurally characterized by gas chromatography-mass spectrometry (neutral and sialylated species) or by tandem mass spectrometry (sulfated species), and a total of 63 structures was assigned. The large intestinal oligosaccharides were found to be identical between the strains, while the small intestinal glycosylation differed. Until now, detailed structural analysis of oligosaccharides isolated from a single mucin core or mucin domain with different origin have not been performed, and the information of different mucin glycoforms has been limited to immunochemistry. Blood group A-determinants (Gal-NAc alpha 1-3(Fuc alpha 1-2)Gal beta 1-, and structures related to the blood group Sd(a)/Cad-related epitope NeuAc/NeuGc alpha 1-3(GalNAc beta 1-4)Gal beta 1-were found in GOT-BW small intestine, and also in both large intestines. Blood group H-determinants and NeuAc/NeuGc alpha 1-3Gal beta 1- were found in all samples. Core 1 (Gal beta 1-3GalNAc alpha 1-), core 2 (Gal beta 1-3(GlcNAc beta 1-6)GalNAc alpha 1-), core 3 (GlcNAc beta 1-3GalNAc alpha 1-), and core 4 (GlcNAc beta 1-3(GlcNAc beta 1-6)GalNAc alpha 1- were also found in all the samples. The large intestine were enriched in sulfated oligosaccharides and the small intestine contained higher amounts of sialylated species. Sulfation were found exclusively on C-6 of GlcNAc.