Mitochondrial diseases are one of the most common forms of inherited neuromuscular disease. The presentations of these diseases are highly variable with both neurological and systemic involvement . Despite progress in identifying mitochondrial DNA mutations that result in disease, the natural history of mitochondrial diseases still remains unclear and no effective treatments are currently available (Pfeffer et al., 2012). The use of numerous primary outcomes in studies has made comparisons between studies difficult. A recent Cochrane review recommended the use of measures that were more relevant to patients in studies. This thesis aims to explore the use physiological measures alongside functional measures and gait in mitochondrial disease. The studies demonstrated that all functional outcome measures were able to discriminate between participants with mitochondrial disease and control subjects. However, gait characteristics were also able to discriminate between the two different mitochondrial genotypes. An aerobic exercise intervention resulted in an improvement in exercise capacity. However, disease severity, functional ability and gait measures remained unchanged. The main findings from this thesis are that: Clinical functional measures and gait are relevant for use in the research and clinical management of mitochondrial disease to monitor disease burden. The improvement in exercise capacity following a cycling intervention was unable to be translated into an improvement in function or gait. Therefore further research into other types of interventions, which may improve activities relevant to patients, is required.