When strabismus is congenital or develops in infancy, it can cause amblyopia, in which the brain ignores input from the deviated eye. Even with therapy for amblyopia, stereoblindness may occur. The appearance of strabismus may also be a cosmetic problem. One study reported 85% of adult strabismus patients "reported that they had problems with work, school, and sports because of their strabismus." The same study also reported 70% said strabismus "had a negative effect on their self-image." A second operation is sometimes required to straighten the eyes.

Medication is used for strabismus in certain circumstances. In 1989, the US FDA approved Botulinum toxin therapy for strabismus in patients over 12 years old. Most commonly used in adults, the technique is also used for treating children, in particular children affected by infantile esotropia. The toxin is injected in the stronger muscle, causing temporary and partial paralysis. The treatment may need to be repeated three to four months later once the paralysis wears off. Common side effects are double vision, droopy eyelid, overcorrection, and no effect. The side effects typically resolve also within three to four months. Botulinum toxin therapy has been reported to be similarly successful as strabismus surgery for people with binocular vision and less successful than surgery for those who have no binocular vision.

Fixation disparity exists when there is a small misalignment of the eyes when viewing with binocular vision. The misaligment may be vertical, horizontal or both. The misalignment (a few minutes of arc) is much smaller than that of strabismus, which prevents binocular vision, although it may reduce a patient's level of stereopsis. A patient may or may not have fixation disparity and a patient may have a different fixation disparity at distance than near.

There are several methods to quantify fixation disparity. The Mallett card, the Bernell lantern slide, the Wesson Card and the Disparometer may be used. A patient's associated phoria is the amount of prism needed to reduce their fixation disparity to zero minutes of arc.

The Mallett Fixation Disparity Unit

Instrument used to measure the associated heterophoria (or compensating prism). It consists of a small central fixation letter X surrounded by two letters O, one on each side of X, the three letters being seen binocularly, and two coloured polarized vertical bars in line with the centre of the X which are seen by each eye separately. The instrument can be swung through 90° to measure any vertical fixation disparity. The associated phoria is indicated by the misalignment of the two polarized bars when the subject fixates the X through cross-polarized filters in front of the eyes. The amount of associated phoria is given by the value of the base-in or base-out prism power necessary to produce alignment and the eye. The unit can also be used to detect suppression. See Disparometer; associated heterophoria; uncompensated heterophoria.

When the fusional vergence system can no longer hold back heterophoria, the phoria manifests. In this condition, the eyes deviate from the fixating position.

Heterophoria is an eye condition in which the directions that the eyes are pointing at rest position, when "not" performing binocular fusion, are not the same as each other, or, "not straight". There can be esophoria, where the eyes tend to cross inward in the absence of fusion; exophoria, in which they diverge; or hyperphoria, in which one eye points up or down relative to the other. Phorias are known as 'latent squint' because the tendency of the eyes to deviate is kept latent by fusion. A person with two normal eyes has single vision (usually) because of the combined use of the sensory and motor systems. The motor system acts to point both eyes at the target of interest; any offset is detected visually (and the motor system corrects it). Heterophoria only occurs during dissociation of the left eye and right eye, when fusion of the eyes is absent. If you cover one eye (e.g. with your hand) you remove the sensory information about the eye's position in the orbit. Without this, there is no stimulus to binocular fusion, and the eye will move to a position of "rest". The difference between this position, and where it would be were the eye uncovered, is the heterophoria. The opposite of heterophoria, where the eyes are straight when relaxed and not fusing, is called orthophoria.

In contrast, fixation disparity is a very small deviation of the pointing directions of the eyes that is present while performing binocular fusion.

Heterophoria is usually asymptomatic. This is when it is said to be "compensated". When fusional reserve is used to compensate for heterophoria, it is known as compensating vergence. In severe cases, when the heterophoria is not overcome by fusional vergence, sign and symptoms appear. This is called decompensated heterophoria.

Heterophoria may lead to squint or also known as strabismus.

While preventive measures, such as taking breaks from activities that cause eye strain are suggested, there are certain treatments which a person suffering from the condition can take to ease the pain or discomfort that the affliction causes. Perhaps the most effective of these is to remove all light sources from a room and allow the eyes to relax in darkness. Free of needing to focus, the eyes will naturally relax over time, and relieve the discomfort that comes with the strain. Cool compresses also help to some degree, though care should be taken to not use anything cold enough to damage the eyes themselves (such as ice). A number of companies have released "computer glasses" which, through the use of specially tinted lenses, help alleviate many of the factors which cause eye strain, though they do not completely prevent it. Rather, they just make it harder to strain the eye.

Esophoria is an eye condition involving inward deviation of the eye, usually due to extra-ocular muscle imbalance. It is a type of heterophoria.

Causes include:

- Refractive errors

- Divergence insufficiency

- Convergence excess; this can be due to nerve, muscle, congenital or mechanical anomalies.

Unlike esotropia, fusion is possible and therefore diplopia is uncommon.

Exophoria can be caused by several factors, which include:

- Refractive errors - distance and near deviation approximately equal.

- Divergence excess - exodeviation is more than 15 dioptres greater for distance than near deviation.

- Convergence insufficiency - near exodeviation greater than distance deviation.

These can be due to nerve, muscle, or congenital problems, or due to mechanical anomalies. Unlike exotropia, fusion is possible in this condition, causing diplopia to be uncommon.

Exophoria is a form of heterophoria in which there is a tendency of the eyes to deviate outward. During examination, when the eyes are dissociated, the visual axes will appear to diverge away from one another.

The axis deviation in exophoria is usually mild compared with that of exotropia.

Sometimes asthenopia can be due to specific visual problems—for example, uncorrected refraction errors or binocular vision problems such as accommodative insufficiency or heterophoria. It is often caused by the viewing of monitors such as those of computers or phones for prolonged periods of time.