Saccharomyces cerevisiae possesses three mitochondrial NADH:ubiquinone oxidoreductases. The rotenone-insensitive internal NADH:ubiquinone oxidoreductase [Ndi1] is solely responsible for the reduction of ubiquinone by mitochondrial matrix-derived NADH during the process of oxidative phosphorylation. Its homologues from Plasmodium and Mycobacterium bear particular relevance to the treatment of malaria and tuberculosis. It has also been proposed as an agent in gene therapy against mitochondrial complex I dysfunction in disease states such as sporadic Parkinsonism. The work presented in this thesis describes the structural analysis of Ndi1 using x-ray crystallography. The structure of Ndi1 was determined by molecular replacement to 2.5 A resolution. The monomer shares the same fold with the glutathione reductase-structural family. It has a unique C-terminal domain, which contains two amphiphatic helices that lie paralell to the membrane and mediate insertion into the top leaf of the lipid bilayer. The structure depicts a parallel homodimeric biological unit with each protomer presenting a hydrophilic and hydrophobic substrate channel. The dimer arrangement positions the substrate channels in the same orientation relative to the membrane. The flavin ring is positioned at the juncture of the two substrate channels. Only its re-face is accessible to nucleophilic attack. Ndi1 was co-crystallised with NAD+ [2.9 A] and ubiqinone-2 [3.0 A]. Ndi1 quinone-binding and activation is likely to be facilitated by two active-site Thr residues. The ping-pong reaction mechanism of Ndi1 is accounted for by the overlap observed between the pyridine and benzoquinone moieties in the ligand-complexes. This mechanism is similar to quinone reductase NQ01.