The necessary biomass pretreatment step, to render the material accessible to the relevant enzyme pool, has been under thorough investigation as the production of biomass syrups, via enzymatic hydrolysis, with high sugars concentrations and yields and low inhibitors concentrations requires the pretreatment to be both efficient and low cost. A good choice for biomass pretreatment should be made by considering: (i) the possibility to use high biomass concentration; (ii) a highly digestible pretreated solid by either increasing the biomass superficial area or decrease in crystallinity or both; (iii) no significant sugar degradation into toxic compounds; (iv) yeast and bacterial fermentation compatibility of the derived sugar syrups; (v) lignin recovery; (vi) operation in reasonably sized and moderately priced reactors and (vii) minimum heat and power requirements [1]. Considering the most known pretreatments, such as diluted acid, hydrothermal processes, steam explosion, milling, extrusion, and ionic liquids, different pretreatment methods produce different effects on the biomass in terms of its structure and composition [2]. For example, the hydrothermal, steam explosion and acidic pretreatments conceptually remove mainly the biomass hemicellulose fraction whereas alkaline pretreatments remove lignin. On the other hand the product of a milling-based pretreatment retains the biomass initial composition. Furthermore, cellulose crystallinity is not significantly reduced by pretreatments based on steam, or hydrothermal, or acidic procedures, whereas ionic liquid-based techniques can shift crystalline cellulose into amorphous cellulose, substantially increasing the enzymatic hydrolysis rates and yields. As such, the choice of pretreatment and its operational conditions as well as the composition of the enzyme blend used in the hydrolysis step, determines the hexose and pentose sugars composition, the concentration and toxicity of the resulting biomass syrups. The activity profile of the enzyme blend and the enzyme load for an effective saccharification may also vary according to the pretreatment. Indeed, a low hemicellulase load can be used for a xylan-free biomass and a lower cellulase load will be needed for the hydrolysis of a low crystalline and highly amorphous pretreated biomass material. As the pretreatment choice will also be affected by the type of biomass, the envisaged biorefinery model will need to consider the main types of biomass that will be used for the biorefinery operation so as to select an appropriate, and versatile pretreatment method [3]. Considering the biorrefinery concept which broadens the biomass derived products, the C6 sugars could be fermented into ethanol, while the C5 stream could be used for the production, via biotechnological routes, of a wide range of chemicals with higher added value. To date, sugarcane and woody biomass, depending on the geographic location, are strong candidates as the main renewable resources to be fed into a biorefinery. However, due to major differences regarding their physical properties and chemical composition, the relevant pretreatments to be used in each case are expected to be selective and customized. Moreover, a necessary conditioning step for wood size reduction, prior to the pretreatment, may not be necessary for sugarcane bagasse, affecting the pretreatment energy consumption and costs. Moreover, the choice of pretreatment should take into account the foreseen utilization of the main biomass molecular components (cellulose, hemicelluloses and lignin). It is important to point out that lignin can be used as a valuable solid fuel or as a source of aromatic structures for the chemical industry. Sugarcane is one of the major agricultural crops when considering ethanol production, especially in tropical countries. In Brazil, sugarcane occupies 8.4 million hectares, which corresponds to 2.4% of farmable lands in Brazil. The gross revenue of this sector is about US$ 20 billion (54% as ethanol, 44% as sugar, and 2% as bioelectricity) [4]. In addition, up to 50% of all vehicles in Brazil are flex fuel cars, which corresponds to approximately 15 million cars [5]. Given the above, Brazil is an important player in this scenario, and, consequently, sugarcane bagasse and straw are promising feed stocks for biomass ethanol. Brazil produced, in 2008, 415 million tons of sugar cane residues, 195 million tons of sugarcane bagasse, and 220 million tons of sugarcane straw, whereas the forecast for the 2011 sugarcane production is 590 million tons, which would correspond to 178 million tons of bagasse, and 200 million tons of straw [6]. Currently, in Brazil, R&D on the use of biomass via biotechnological routes has been focused mainly on agricultural residues such as sugarcane residual biomass.