Advanced generation biofuel production from lignocellulosic material (LCM) was investigated. A range of different thermo-chemical pre-treatments were evaluated with different LCM. The pre-treatments included; alkaline (5% NaOH at 50°C), acid (1% H2SO4 at 121°C) and autohydrolytical methods (200°C aqueous based hydrothermal) and were evaluated using samples of miscanthus, wheat-straw and willow. The liberation of sugars, presence of inhibitory compounds, and the degree of enhancement of enzymatic saccharification was accessed. The suitability of the pre-treatment generated hydrolysates (as bioethanol feedstocks for Saccharomyces cerevisiae) was also accessed using a phenotypic microarray that measured yeast metabolic output. The use of the alkaline pre-treatment liberated more glucose and arabinose into both the pre-treatment generated hydrolysate and also the hydrolysate produced after enzymatic hydrolysis (when compared with other pre-treatments). However, hydrolysates derived from use of alkaline pre-treatments were shown to be unsuitable as a fermentation medium due to issues with colloidal stability (high viscosity). Use of acid or autohydrolytical pre-treatments liberated high concentrations of monosaccharides regardless of the LCM used and the hydrolysates had good fermentation performance with measurable yeast metabolic output. Acid pre-treated wheat straw hydrolysates were then used as a model system for larger scale fermentations to confirm both the results of the phenotypic microarray and its validity as an effective high-throughput screening tool.