Conventional magnetic resonance imaging (MRI) is useful for assessing morphological changes but not for assessing deformations inside homogeneous structures (M. D. Abràmoff, A. P. Van Gils, G. H. Jansen, & M. P. Mourits, 2000). Since no intrinsic contrast can be imaged for distinguishing heterogeneous patterns of muscle contraction, morphological changes along the length of the extraocular muscles (EOMs) are not macroscopically detectable. However, an imaging method that is able to directly encode motion could give evidence about the dynamics of the inhomogeneous deformation of the EOMs. Thus, we developed a method for acquiring motion-encoded MRI images of the EOMs during eye movements. Seven healthy subjects gazed at a horizontal sinusoidally oscillating target. A small surface coil was placed in front of the right orbit. The contracting and relaxing horizontal rectus muscles and the noncontracting optic nerve were reliably tracked. The differential contractility of the EOMs could be distinguished from the third time frame on (=140 ms from the beginning of the right to left eye movement lasting 1 s). The muscle belly of the contracting medial rectus muscle could be distinguished from the posterior and the anterior segment from the sixth time frame on (=350 ms). In conclusion, motion-encoded MRI resolved the heterogeneous contraction of moving EOM segments in healthy subjects without using physical markers.