The branched-chain aminotransferase is a pyridoxal 5′-phosphate (PLP)-dependent enzyme responsible for the final step in the biosynthesis of all three branched-chain amino acids, L-leucine, L-isoleucine, and L-valine, in bacteria. We have investigated the mechanism of inactivation of the branched-chain aminotransferase from Mycobacterium tuberculosis (MtIlvE) by D- and L-cycloserine. D-Cycloserine is currently used only in the treatment of multidrug–drug-resistant tuberculosis. Our results show a time-and concentration-dependent inactivation of MtIlvE by both isomers, with L-cycloserine being a 40-fold better inhibitor of the enzyme. Minimum inhibitory concentration (MIC) studies revealed that L-cycloserine is a 10-fold better inhibitor of Mycobacterium tuberculosis growth than D-cycloserine. In addition, we have crystallized the MtIlvE-D-cycloserine inhibited enzyme, determining the structure to 1.7 Å. The structure of the covalent D-cycloserine-PMP adduct bound to MtIlvE reveals that the D-cycloserine ring is planar and aromatic, as previously observed for other enzyme systems. Mass spectrometry reveals that both the D-cycloserine- and L-cycloserine-PMP complexes have the same mass, and are likely to be the same aromatized, isoxazole product. However, the kinetics of formation of the MtIlvE D-cycloserine-PMP and MtIlvE L-cycloserine-PMP adducts are quite different. While the kinetics of the formation of the MtIlvE D-cycloserine-PMP complex can be fit to a single exponential, the formation of the MtIlvE L-cycloserine-PMP complex occurs in two steps. We propose a chemical mechanism for the inactivation of D- and L-cycloserine which suggests a stereochemically determined structural role for the differing kinetics of inactivation. These results demonstrate that the mechanism of action of D-cycloserine’s activity against M. tuberculosis may be more complicated than previously thought and that D-cycloserine may compromise the in vivo activity of multiple PLP-dependent enzymes, including MtIlvE.