This is the first study to measure EOM T2 in a genetically homogenous CPEO cohort. While acute inflammation prolongs T2, and is used to quantify EOM inflammation in thyroid-related ophthalmopathy [15–19], inflammation is unlikely to be a pathological substrate of EOM T2 change in CPEO, since inflammatory infiltrates are usually absent in the muscle biopsies of patients with mitochondrial disease. This is supported by the predominant absence of EOM STIR hyperintensities in our patient images, and suggests increased intramuscular lipid as the source of T2 elevation since our T2 relaxometry acquisition was not fat-suppressed. A further analysis (results not shown) that attempted to fit a bi-exponential model to the multi-echo decay data was not sufficient to obtain putative lipid and muscle-water components with independent T2 values, and more sophisticated future measurements will be required to unambiguously establish the origin of the total muscle T2 elevation. A further caveat to interpretation of the T2 findings is the potential susceptibility of the measurements to contamination from the surrounding fatty substrate, despite our precautions in defining conservative ROI boundaries. Nevertheless, elevated patient EOM T2 compared with controls was consistent and, coupled with the correlation observed between EOM T2 and ROEM measures, should motivate future more sophisticated investigations.