Biomass fractionation into its individual building blocks poses a major challenge to the biorefinery concept. The recalcitrance of the lignocellulose matrix and the high crystallinity of cellulose make typical feed stocks difficult to separate into their components. Hydrothermal processing fractionates biomass by its hydrolysis. However, a deep knowledge of hydrolysis principles is required since an inappropriate selection of the operating parameters such as an excessive temperature and a long residence times causes dramatic selectivity losses. This review is divided in four main sections which present the fundamentals of lignocellulosic biomass fractionation in hemicelluloses, cellulose and lignin. As the biomass structure plays an important role, a section to study the extraction of the linked phenols that joint lignin and hemicelluloses is included.