Agricultural and forest waste products are abundant and low-cost biomass sources useful in renewable fuel energy and feedstock preparation. Hydrolysis of a major biomass component, hemicellulose, is accomplished by the action of endo-xylanases. Reaction products vary in composition and degree of polymerization as a function of both feedstock and the enzyme activities utilized, ranging from monomeric sugars to complex branched polysaccharides. The study herein describes heterologous expression in Aspergillus awamori of a betabeta-(1-4) endo-xylanase isolated from the whole-genome DNA sequence of A. clavatus along with a comprehensive biochemical and functional analysis of the enzyme, including substrate preference and hydrolysis patterns. The A. clavatus xylanase promotes incomplete hydrolysis of xylan substrates resulting in xylobiose, xylotriose and xylotetraose. Incomplete degradation resulting in xylo-oligomers is appealing for functional foods as the beneficial effect of oligosaccharides on gastrointestinal micro flora includes preventing proliferation of pathogenic intestinal bacteria and facilitating digestion and absorption of nutrients.