Background With the technical advances, magnetic resonance imaging (MRI) is now sensitive enough to detect subtle structural abnormalities of ocular motor nerves arising from the brainstem and orbits of living subjects. This study was designed to delineate the MRI characteristics in patients with special forms of strabismus. Methods A total of 29 patients with special forms of strabismus underwent orbital and intracalvarium MRI. Imaging of the ocular motor nerves in the brainstem was performed in 0.8 mm thickness image planes using the three-dimensional fast imaging employing steady-state acquisition (3D-FIESTA) sequence. Nerves to extraocular muscles (EOMs), EOMs and their associated connective tissues were imaged with T1 weighting in tri-planar scans by dual-phased coils within 2.0 mm thick planes. Results Patients with congenital fibrosis of the extraocular muscles exhibited hypoplasia of the oculomotor (CN3), abducens (CN6), trochlear (CN4) nerves, and the EOMs; hypoplasia of CN6 in the brainstem and an extra branch of the inferior division of CN3 to the lateral rectus were the most common but not the only presentation of Duane's retraction syndrome. Hypoplasia of CN6, facial (CN7) and hypoglossal (CN12) nerves were revealed in patients with Mobius syndrome. In a rare case of bilateral synergistic convergence and divergence, an enlarged branch of CN3 to the medial rectus and a questionable branch of CN3 to the inferior rectus bilaterally were found. Conclusion MRI can reveal subtle structures of the ocular motor nerves and their corresponding EOMs. This can provide valuable information regarding pathogenesis in some special forms of strabismus. Chin Med J 2009;122(24):2998-3002