The localization of extraocular motoneurons in the rat was investigated by injecting horseradish peroxidase and [125I]wheat germ agglutinin as retrograde tracer substances into individual eye muscles. The organization of subnuclei was found to be most similar to the rabbit. The subgroups representing the medial rectus and inferior rectus muscles are located in the rostral two thirds of the ipsilateral oculomotor nucleus (nIII) with some medial rectus motoneurons scattered laterally along the edge of the medial longitudinal fasciculus. The motor pool controlling the inferior oblique muscle is located in the middle third of the ipsilateral nIII. The motoneurons of the superior rectus muscle are in the caudal two-thirds of contralateral nIII while the levator palpebrae muscle has a bilateral innervation in the oculomotor nucleus. The motoneurons of the superior oblique are located in the contralateral trochlear nucleus although a few labeled neurons were scattered laterally in amongst the fibers of the medial longitudinal fasciculus. The cell bodies of lateral rectus motoneurons are not homogeneously distributed throughout the ipsilateral abducens nucleus. A regional separation between the latter and internuclear neurons was found after injecting HRP into the oculomotor nucleus.