Carbohydrate chains in glycoconjugates play important roles in various life phenomena, and there are numerous types of recognition system for carbohydrate chains due to carbohydrate-lectin interactions/carbohydrate-carbohydrate interactions in all higher life forms. It has been proposed that macromolecular polysaccharides isolated from plants, marine organisms, or fungi cross-interact with known and unknown recognition systems in mammals to express their pharmacological activities. Therefore the elucidation of carbohydrate structures related to the activities and functions of these polysaccharide molecules will lead us to utilize the related information in the development of novel carbohydrate-based drugs and functional foods for human health care. Peyer's patches present in the upper intestinal tract play important roles as inductive sites for both protective IgA production and immune tolerance induction in mucosal and systemic immune systems. Dysfunction of the immunocompetent cells of Peyer's patches is thought to induce allergic/autoimmune diseases and down-regulation of the protective system against infectious agents on mucosal sites. We have isolated several Peyer's patch cell-modulating polysaccharides from medicinal herbs used in traditional Japanese herbal remedies, and they have been assumed to comprise the responsible carbohydrate chains with oligosaccharide sizes for expression of modulating activity. Accumulation of knowledge on the structures and functions of these responsible carbohydrate chains in polysaccharide molecules is believed to be important for the development of methodology for logically factitious regulation of functions of immunocompetent cells in Peyer's patches. This review deals with recent results of our study on the structural clarification of responsible carbohydrate chains in modulating polysaccharides against functions of immunocompetent cells in Peyer's patches.