Biomass pre-treatment is a key first step in converting recalcitrant lignocellulosic biomass into value-added products. Aqueous hydroxide solutions can be effective biomass pre-treatment media, and the cation of the hydroxide salt can have an extremely significant effect upon the physicochemical behaviour of the hydroxide solution. However, the cation effect has not been comprehensively investigated with respect to biomass pre-treatment. Here we have investigated pre-treatment of rice husks (from Oryza sativa) and shown that the cation indeed has a significant effect upon downstream enzymatic hydrolysis of the cellulose (with cellulase). In particular, the ability of the solution to dissolve cellulose was negatively correlated with pretreatment effectiveness, as judged by the downstream glucose yield. This was observed by investigating aqueous solutions of lithium, potassium, caesium, tetramethylammonium, tetraethylammonium, tetrapropylammonium, tetrabutylammonium and tetrahexylammonium hydroxide. Silica solubility was almost cation-independent, lignin solubility was moderately cation-dependent, while cellulose solubility was strongly cation-dependent. The rate of lignin extraction was inversely correlated with the size of the cation. As cellulose-dissolution is a demanding chemical process, it initially limited the ability of the solution to disrupt the whole biomass, necessitated extensive washing of the pre-treated rice husk, and still resulted in significant cation contamination downstream. Overall, lithium hydroxide was found to be the most effective hydroxide.