Three mechanisms proposed for the triosephosphate isomerase (TIM) catalyzed reactions were studied with the QM/MM approach using B3LYP/6-31+G(d,p) as the QM method. The two pathways that involve an enediol species were found to give similar values for the barriers and the calculated rates are in satisfactory agreement with experiment. By contrast, the mechanism that involves intramolecular proton transfer in the enediolate was found to be energetically unfavorable due to electrostatic interactions with His 95, a conserved residue in TIM from different organisms. A perturbation analysis was used to determine the residues that make the major contribution to catalysis.