The enzymatic hydrolysis of cellulose in ionic liquid (IL) containing systems has recently received a lot of interest as a pretreatment in biomass conversion to liquid biofuels and chemicals. In this paper we present a study in which the activity and action of two Trichoderma reesei endoglucanases, Cel7B and Cel5A, were evaluated in aqueous solutions containing 0–90% (v/v) of the ionic liquids 1,3-dimethylimidazolium dimethylphosphate or 1-ethyl-3-methylimidazolium acetate, using microcrystalline cellulose (Avicell) as a model substrate. The degree of hydrolysis was analysed by capillary electrophoresis of the hydrolysates and gel permeation chromatography of the remaining cellulose residues. Both of the employed ionic liquids severely inactivated the T. reesei endoglucanases. Only traces of soluble oligosaccharides were present in hydrolysis mixtures containing 40% (v/v) or more of ionic liquids. The employed ILs were found to have a basic impact on the hydrolysis environment, but it could be concluded that the basicity of the ILs was not the only reason for the cellulase inactivation. The effect of an IL on the cellulose binding module in Cel5A was evaluated by comparing the hydrolysis yields of the intact Cel5A and the Cel5A core lacking the cellulose binding module. In this study the cellulose binding module was found to be the most ionic liquid sensitive part of the enzymes used. Comparative data from the partial hydrolysis of an ionic liquid regenerated cellulose is also reported.