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In an integrated biorefinery concept, biological hydrogen and methane production from lignocellulosic substrates appears to be one of the most promising alternatives to produce energy from renewable sources. However, lignocellulosic substrates present compositional and structural features that can limit their conversion into biohydrogen and methane. In this study, biohydrogen and methane potentials of 20 lignocellulosic residues were evaluated. Compositional (lignin, cellulose, hemicelluloses, total uronic acids, proteins, and soluble sugars) as well as structural features (crystallinity) were determined for each substrate. Two predictive partial least square (PLS) models were built to determine which compositional and structural parameters affected biohydrogen or methane production from lignocellulosic substrates, among proteins, total uronic acids, soluble sugars, crystalline cellulose, amorphous holocelluloses, and lignin. Only soluble sugars had a significant positive effect on biohydrogen production. Besides, methane potentials correlated negatively to the lignin contents and, to a lower extent, crystalline cellulose showed also a negative impact, whereas soluble sugars, proteins, and amorphous hemicelluloses showed a positive impact. These findings will help to develop further pretreatment strategies for enhancing both biohydrogen and methane production.