While EOM cross-sectional area has previously been investigated in CPEO, correlations between muscle dimensions and other quantitative MRI measures, and clinical functional measurements, have not been reported. Such correlations, if observed, would support the validity of MRI measures as biologically relevant disease indices. Although we found no correlation between muscle atrophy and reduced ROEM or disease duration, there was a significant negative correlation between T2 and ROEM in the patients. This indicates that although measures relating to EOM volume may not be useful to quantify severity in patients with long-established disease, measures such as EOM T2, reflecting variations in muscle composition rather than size, may provide valid alternative functionally relevant markers. Future studies will be required to establish the sensitivity of EOM T2 to longitudinal change, and to establish the sensitivity of the measure to partial volume confounds due to surrounding intra-orbital fat.