Key Points • Chronic progressive external ophthalmoplegia is a common clinical manifestation of mitochondrial disease. • Existing extra-ocular muscle MRI data in CPEO reports variable radiological findings. • MRI confirmed EOM atrophy and characteristic signal changes in CPEO. • EOM T2 was significantly elevated in CPEO and correlated negatively with ocular movements. • EOM T2 represents a potential quantitative measure of disease severity in CPEO.