Strabismus, or misalignment of the eyes, is a common ophthalmic problem in childhood, affecting 2 to 5% of the preschool population. Amblyopia is an important cause of visual morbidity frequently associated with strabismus, and both conditions should be treated simultaneously. Pharmacological means for treating strabismus and amblyopia can be divided into 3 categories: paralytic agents (botulinum toxin) used directly on the extraocular muscles to affect eye movements; autonomic agents (atropine, miotics) used topically to manipulate the refractive status of the eye and thereby affect alignment, focus and amblyopia; and centrally acting agents, including levodopa and citicoline, which affect the central visual system abnormalities in amblyopia. Botulinum toxin, the paralytic agent that causes the clinical symptoms of botulism poisoning, can be injected in minute quantities to achieve controlled paralysis of the extraocular muscles. Although the role of botulinum toxin is established in adults with paralytic strabismus, its usefulness in the treatment of comitant childhood strabismus (primary esotropia and exotropia) is not universally accepted. Botulinum injections tend to be more effective with smaller degrees of strabismus, in patients with good binocular fusion, and in managing overcorrections or undercorrections after traditional muscle surgery. Inadvertent ptosis and paralysis of adjacent muscles, unpredictable responses and technical constraints of the injections limit its use in children. Miotic therapy, by altering the refractive state of the treated eye, offers an alternative to optical correction with bifocals in treating esotropia due to excessive accommodative convergence. It is also effective in treating residual esotropia following surgery. The ease of use of glasses restricts the wide application of miotics in these common strabismus syndromes. Atropine, an anticholinergic agent, paralyses the ability of the eye to focus or accommodate. In amblyopia therapy, atropine is used to blur vision in the non-amblyopic eye and offers a useful alternative to traditional occlusion therapy with patching, especially in older children who are not compliant with patching. The neurotransmitter precursor levodopa and the related compound citicoline have been demonstrated to improve vision in amblyopic eyes. The therapeutic role of these centrally acting agents in the clinical management of amblyopia remains unproven.