The modification of the lignin structure of an eucalyptus feedstock during alkaline delignification by kraft, soda-AQ, and soda-O2 cooking processes has been investigated by different analytical techniques (size exclusion chromatography (SEC), pyrolysis gas chromatography-mass spectroscopy (Py-GC/MS), 1H-13C two-dimensional nuclear magnetic resonance (2D-NMR), and 31P NMR). The characteristics of the lignins were compared at different pulp kappa levels, and with the native lignin isolated from the wood. The structural differences between the kraft, soda-AQ, and soda-O2 residual lignins were more significant at earlier pulping stages. At the final stages, all the lignin characteristics were similar, with the exception of their phenolic content. Strong differences between lignins from pulps and cooking liquors were observed, including enrichment in guaiacyl units in pulp residual lignin and enrichment in syringyl units in black liquor lignin. A comparison of the alkaline cookings indicate that soda-O2 process produced higher lignin degradation and provided promising results as pretreatment for the deconstruction of eucalyptus feedstocks for subsequent use in lignocellulose biorefineries. © 2013 American Chemical Society. ; 11 páginas.-- 5 figuras.-- 4 tablas.-- 50 referencias.-- Supporting Information The general conditions for the kraft, soda-AQ, and soda-O2 alkaline cooking of eucalyptus feedstock, are shown in Table S1. The identification and relative molar abundance of the compounds identified in the Py-GC/MS of MWL from eucalyptus wood, and residual and black liquor lignins from kraft, soda-AQ,and soda-O2 pulping at different kappa numbers, are listed in Table S2. This material is available free of charge via the Internet at http://pubs.acs.org/doi/suppl/10.1021/ie401364d ; This study has been funded by the EU-Project LIGNODECO (No. KBBE-244362), the Spanish project (No. AGL2011-25379), and the CSIC project (No. 201040E075). Dr. Rencoret thanks the CSIC for a JAE-DOC contract in the program “Junta para la Ampliación de Estudios”, cofinanced by Fondo Social Europeo (FSE). Finally, we thank Suzano Papel e Celulose (Brazil) for providing the pulp and black liquor samples from the alkaline cooking experiments and the corresponding additional data.