Changes in the structural, molecular and functional properties of the immunogenic corn cob xylan evoked by ultrasonication in water, 1% NaOH and 5% NaOH were investigated. The reduction of the high molar mass (MM) fraction was more intense than that of the medium MM fraction, depending on the sonic power, sonication time, and alkali concentration. The chain degradation was more effective in the alkaline media. The UV-absorbing component, accompanying the xylan polymers in the whole MM range, showed an accumulation in the high MM region as well as shiftening to higher sizes, particularly in 5% NaOH. The sugar composition and primary structure of the xylan was almost retained under all irradiation conditions studied. Although the biological activity of the xylan was affected by the ultrasound, no significant decrease of the biological response was found at short irradiation time and low sonic power.