The structure/function relationship of two acidic heteroxylan types, the arabino-(glucurono)xylan from corn cobs (AGX) and 4-O-methylglucuronoxylans (GXs) from beechwood and three medicinal herbs (Rudbeckia, Altheae, and Mahonia), has been studied. The effect of the molecular mass of AGX, as well as the content and distribution of the 4-O-methylglucuronic acid side chains in GXs on the immunological activity of these xylans was characterized by their biological response in the mitogenic and comitogenic thymocyte in vitro tests. Depolymerization of AGX by ultrasonication resulted in unequivocal decrease of the immunomodulatory activity, whereas already a short treatment by endo-beta-1,4-xylanase brought about a significant increase in its activity when applied in the highest dose. In the case of the GX samples, neither the uronic acid content nor the distribution pattern of the uronic acid side chains was found to be determinant for the expression of their immunomodulatory activity.