BACKGROUND Chronic progressive external ophthalmoplegia (CPEO) is characterized by slowly progressive bilateral ophthalmoplegia and blepharoptosis. Molecular diagnosis is problematic because sporadic mitochondrial DNA deletions can be causative. We sought findings using magnetic resonance imaging (MRI) that might support the diagnosis of CPEO. METHODS Two men (ages 31 and 47 years) and 3 women (ages 40-49 years) with CPEO and symptom durations of 8 months to 28 years underwent high-resolution (2-mm slice thickness, 312 micron pixels), surface coil, T1-weighted orbital MRI in coronal planes. Images were analyzed quantitatively to determine extraocular muscle (EOM) sizes and were compared with 10 age- and gender-matched normal volunteers, one subject with myasthenia gravis, and with 30 subjects having EOM paralysis caused by oculomotor, trochlear,0 and abducens neuropathies. RESULTS EOM function was clinically diminished in CPEO, most markedly for the superior rectus (SR) and levator muscles. All EOMs in CPEO exhibited unusual qualitative T1 MRI signal abnormalities. Unlike the profound EOM atrophy typical of neurogenic paralysis, anterior volumes of medial rectus, lateral rectus, and inferior rectus muscles in CPEO were not smaller than normal (p>0.003). Anterior volumes of the SR muscle-levator complex and superior oblique were significantly reduced (p<0.003). Denervated EOMs exhibited statistically significant volume reduction when compared with normal and CPEO groups. Volume of the SR muscle-levator complex was the same in subjects with CPEO and oculomotor palsies. CONCLUSIONS CPEO is associated with minimal EOM volume reduction despite clinically severe weakness. This combination of findings may be specific for CPEO and could resolve the diagnostic dilemma in difficult cases.