Two methods are used for the isolation of residual lignin: acidolytic and enzymatic hydrolysis. Recently a two-step procedure that is a combination of enzymatic and acidic hydrolyses was proposed. In this paper, the structures of residual lignins isolated by these three methods are compared. Enzymatic hydrolysis gave lignin with the highest yield (83%); however, it contained high amounts of carbohydrates and protein. The molar mass of enzymatic lignin was the highest, indicating that no cleavage of lignin occurred. Acidolysis gave a significantly lower lignin yield (40%), but this lignin was practically free from impurities. The β-aryl ether and lignin-carbohydrate linkages cleaved during the isolation, which was manifested in the decreased molar mass of the lignin as well as in increased phenolic hydroxyl group content. The new two-step isolation procedure gave properties between the preparations of enzymatic and acidolytic hydrolyses. The lignin yield was high (78%), but it contained some impurities, although less than the enzymatic lignin. The lignin-carbohydrate linkages cleaved to some extent, but the β-aryl ether linkages remained intact.