Accurate, valid and reliable biomarkers of disease progression are lacking in mitochondrial disease but will be required to assess the efficacy of novel therapies in treatment trials. We have demonstrated the feasibility of quantitative MRI to provide measures reflecting disease severity in individual EOMs in patients with CPEO. While EOM atrophy is a clear radiological feature, its uniformity in patients and lack of correlation with ROEM suggests it might not provide a meaningful measure of progression in patients studied a significant time after disease onset. In contrast, EOM T2 prolongation was associated with cross-sectional variations in ROEM in our study group, and so may represent a useful biomarker for future clinical trials involving patients with similar disease durations. Future investigations will evaluate the added value of combining T2 measurement with the technically challenging but promising approach of EOM quantitative diffusion weighted imaging [19].