The effect of ionic strength/sodium ion concentration and type of anions on the delignification rate, the retention of xylan and the reactions of hexenuronic acid during kraft cooking has been investigated. A novel, small, flow-through digester was used in the cooking experiments in order to prevent the resorption of lignin and xylan and to maintain a constant concentration of active chemicals throughout the kraft cook. An increase in ionic strength/sodium ion concentration in the cooking liquor decreases the removal rate of both lignin and xylan during kraft cooking. In general, the removal rate of xylan tends to correlate with the delignification rate. However, the present investigation finds that the retention of xylan at a given degree of delignification increases at high ionic strength/sodium ion concentration. The addition of sodium salts of carbonate or chloride to the cooking liquor was shown to increase the rate of formation/degradation reactions of hexenuronic acids and the total amount of uronic acids substituted on the xylan backbone decreases when the concentration of sodium ions increases in the cooking liquor. This promotes a decrease in the dissolution of xylan and consequently an increase in the retention of xylan in the wood residues. The obtained results demonstrate that the xylan content in the fiber wall increases at higher ionic strength/sodium ion concentration, which leads to a slight increase in pulp yield.