Endothiapepsin is derived from the fungus Endothia parasitica and is a member of the aspartic proteinase class of enzymes. This class of enzyme is comprised of two structurally similar lobes; each lobe contributes an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. Knowledge of the protonation states of these aspartates in the tetrahedral intermediate state would determine the catalytic mechanism by which the enzyme operates. The three dimensional structure of endothiapepsin bound to the transition state analogue inhibitor H261 has been solved to high resolution (2.1A) using quasi Laue neutron diffraction. At the time of writing this is the largest protein structure determined at high resolution using neutron diffraction. The position of deuterium atoms in the active site indicates that the outer oxygen of Asp215 and the inhibitory hydroxyl group are protonated in the transition state analogue complex. The three dimensional structures of endothiapepsin bound to five transition state analogue inhibitors (H189, H256, CP-80, 794, PD-129, 541 and PD-130,328) have also been solved using X-rays to atomic resolution allowing full anisotropic modelling of each complex. The structure of endothiapepsin complexed with the gem-diol based inhibitor PD-135, 040 has also been solved to a resolution of 1.6A. The active sites of the six structures have been studied with a view to studying the catalytic mechanism of the aspartic proteinases by locating the active site protons by carboxyl bond length differences and electron density analysis. In the CP-80, 794 structure there is excellent electron density for the hydrogen on the inhibitory statine hydroxyl group which forms a hydrogen bond with the inner oxygen of Asp 32. A number of short hydrogen bonds that may have a role in catalysis (~2.6 A) have been identified within the active site in each structure; the presence of these bonds has been confirmed using NMR techniques.