Over the past several years, we have examined the chemistry of acid pretreatment focusing on the ultra-structure of cellulose, lignin functionality and hemicellulose in the bulk and surface of poplar and switchgrass.  From these studies a re-occurring theme is that acid pretreatments typically increase overall crystallinity and changes the relative  amounts of amorphous and paracrystalline cellulose along with I_a and I_b while decreasing the DP of cellulose.  The polysaccharide component of biomass has also been recently shown to generate pseudo-lignin which increases the residual Klason content after pretreatment, possibly impacting enzymatic deconstruction. Accompanying these changes in carbohydrate chemistry, lignin is changed during pretreatment leading to decreases in b–O-aryl ether, increase in polydispersity and condensed lignin.  Surface studies by ToF-SIMS have shown that surface pretreatment chemistry is uniquely different from bulk chemistry especially in residual hemicelluloses. This presentation will examine these chemical reactions, identify what established reactions suggest about acid pretreatment chemistry, and suggest what  reaction chemistries need further investigation to enhance pretreatment effectiveness and facilitate the next generation of low-recalcitrance engineered crops, better pretreatments, and advanced biocatalysts.