Mitochondria are the powerhouses of eukaryotic cells. Located in the cytoplasm, the double membrane bound organelle generates vast quantities of ATP through a process of oxidative phosphorylation. The pathway consists of five large membrane-bound proteins, which are housed in the invagination of the inner mitochondrial membrane called cristae. The structure of the cristae varies both between species and between different types of tissues within the same organism. In addition, changes in cristae structure are associated with many human diseases. Using a process of electron cryo-tomography and sub-tomogram averaging, we are investigating the molecular basis of cristae structure and function. So far, we have discovered that the membrane-proteins of the oxidative phosphorylation pathway are spatially separated in cristae. The ATP synthases form rows of dimers along highly curved ridges in the cristae membrane while the respiratory chain complexes interact forming supercomplexes in the flat membrane regions. The structures of these complexes are species specific and variation in the morphology of ATP synthase dimer rows correlate with changes in cristae structure. Using a combination of mutations and reconstitution experiments, we have shown that the ATP synthases directly cause membranes to bend and influence cristae structure and organisation. In addition, using the technique of single particle electron cryo-microscope we have determined the structure of a mitochondrial ATP synthase dimer to 6-7Å resolution. This resolution was sufficient to reveal a bundle of four horizontal membrane-intrinsic helices adjacent to the rotor-ring and a pair of offset hydrophilic half-channels extending from the lumen and the matrix to the centre of the horizontal helical bundle. When combined, these results provide a preliminary model for cristae biogenesis in mitochondria and an explanation of how proton movement through the ATP synthase drives rotary catalysis.