Mitochondria are intracellular organelles surrounded by a double membrane. The inner mitochondrial membrane consists of subcompartiments called cristae and the inner boundary membrane. The main function of mitochondria is to generate energy, in the form of adenosine triphosphate (ATP). This is achieved by the oxydative phosphorylation, OXPHOS, located in the cristae. Mutations in the OXPHOS subunits lead to extreme heterogeneity of inherited mitochondrial disorders. Mitochondria are organized in a dynamic connected network within the cells, constantly adapting to cellular requirements by changing its shape and position through processes of fission and fusion. The coordination of the assembly of proteins complexes such as OXPHOS influences the architecture of the mitochondrial cristae and so, the efficiency of mitochondrial ATP production. The key players in cristae morphology include the MICOS complex and the mitochondrial ATP synthase, whose oligomers are retrieved on the edges of the cristae and contribute to define cristae curvature. The number of cristae per mitochondrion, the shape of the cristae, the number of cristae junctions with the peripheral inner mitochondrial membrane are essential structural information we need to assess mitochondrial phenotype. Furthermore, the inner membranes of mitochondria are continuously undergoing remodelling and this new area, recently accessible with the help of super-resolution microscopy, raises many questions regarding the relationship between inner membrane dynamics and the efficiency of ATP production by mitochondria. Mitochondria defects have been involved in many human diseases, such as neurodegenerative disorders, cardiomyopathies and also in cancer. Super-resolution imaging opens up a new field of research by exploring inner membrane remodelling and the content and distribution of inner membrane proteins in a pathological context.