In mammalian brain tissue, most hexokinase is bound to the mitochondria and only a small amount of the enzyme is present in soluble form. In this study we report that, in rabbit brain, hexokinase is present in two distinct molecular forms, which we designated HKH and HKL, both of which are separable using hydrophobic interaction or anion-exchange chromatography. These two molecular forms can be detected when hexokinase is prepared at pH 7.4, whereas at pH 10.0 only the more hydrophobic form, HKH, is present. The two subtypes of hexokinase do not show significant differences in Km values for glucose and ATP, in Ki values for glucose-6-phosphate or in their molecular weights. HKH is able to rebind mitochondrial membranes, while HKL has lost this ability, suggesting that the hydrophobic peptide at the N-terminal has been removed. The susceptibility of the N-terminal peptide to proteolysis is completely inhibited by using antiproteolytic compounds, such as leupeptin or E-64. The results reported in this paper suggest that a cysteine protease, probably belonging to a the class of cathepsins, may be involved in the processing of bindable hexokinase to the non-bindable form in rabbit brain, and that the activity of this protease is pH-dependent.