The ultrastructure of the extraocular muscles of patients affected by congenital strabismus is not completely known, and the structures responsible of the pathogenesis of this condition are still to be determined. Specimens obtained from patients suffering from congenital strabismus were studied and compared with specimens obtained from patients enucleated for various pathologies and not affected by any disorder in the oculomotor system. The scleral myotendinous junction, where the occurrence of an altered proprioceptive innervation was already reported, was examined, and findings obtained were compared with those observed in the muscle body (venter), where motor innervation is prominent and usually described as normal. Only a small number of damaged muscle fibers was found everywhere. The damage consisted in alterations of both contractile structures and mitochondria and resulted in severer lesions in the scleral myotendinous junction rather than in the muscle body. The normal muscle fibers were innervated by motor nerve endings with normal features and by few altered proprioceptors. The less damaged muscle fibers were innervated by normal motor nerve endings and severely damaged proprioceptors. The most severely damaged muscle fibers did not receive any type of innervation. These data seem to imply that the most important functional alteration in strabismus regards the scleral myotendinous junction. It is the authors’ opinion that these findings might have a clinical importance in choosing the treatment to be pursued in patients with a squint.