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We established a method for producing two types of xylooligosaccharides by treating kraft pulp derived from hardwood such as eucalyptus with xylanase, analyzed the structure by MALDI-TOF-MS/MS, and conducted an in vitro study on utilization by intestinal bacteria. One type was a neutral xylooligosaccharide (XOS), a xylooligomer in the D.P. range of dimer to approximately 17-mer, containing approximately 12% xylobiose. The other was an acidic xylooligosaccharide (U-XOS), a xylooligomer in the D.P. range of dimer to approximately 17-mer, with a major side chain of 4-O-methyl-glucuronic acid and other side chains of glucuronic acid and 2-O-galactopyranosyl-4-O-methyl-glucurono acid. The in vitro utilization study with intestinal bacteria showed that XOS was specifically utilized by Bifidobacterium, whereas U-XOS was utilized by only a few types of bacteria. In a fecal batch culture, both XOS and U-XOS selectively increased the population of Bifidobacterium. The present study proposes a new method for industrial production of XOS and U-XOS, and indicates the utility and functionality.