AbstractAimInulooligosaccharides in a Kampo formula, hochuekkito, have been shown to participate in the regulation of the pulmonary immune system. Difference in chain length distribution of the oligosaccharides strongly affects their immunopharmacological activities. This phenomenon cannot be explained by bifidogenic activity and/or short‐chain fatty acids produced by intestinal microflora from the oligosaccharides. Effects of intermediate‐size inulooligosaccharides, which have a similar chain length distribution as the oligosaccharides obtained from hochuekkito containing Atractylodis rhizoma, were analyzed on immunocompetent cells in Peyer’s patches.MethodsEffect of intermediate‐size inulooligosaccharide preparation (degree of polymerization (d.p.) 3–15) on mRNA expression of genes of markers and functional molecules of stromal cells and type 3 innate lymphoid cells (ILC3) in Peyer’s patches was analyzed.ResultsOral administration of intermediate‐size inulooligosaccharide preparation significantly up‐regulated expression of mRNAs of genes of not only marker molecules of fibroblastic reticular cells (FRC) and ILC3 but also immunological factors for positive and negative regulatory functions of FRC in addition to genes of auto‐immune regulator (AIRE), DEAF‐1 transcription factor, and some AIRE‐dependent tissue‐related antigens (TRA).ConclusionFRC and ILC3 are suggested to be target cell candidates in Peyer’s patches for inulooligosaccharides in hochuekkito formula containing Atractylodis rhizoma.