Many environmental conditions have also been known to cause anophthalmia. The strongest support for environmental causes has been studies where children have had gestational-acquired infections. These infections are typically viral. A few known pathogens that can cause anophthalmia are Toxoplasma, rubella, and certain strains of the influenza virus. Other known environmental conditions that have led to anophthalmia are maternal vitamin A deficiency, exposure to X-rays during gestation, solvent abuse, and exposure to thalidomide.

The number of cases is around 0.5 to 0.7 per 10,000 births, making it a relatively rare condition.

An interstitial deletion of chromosome 14 has been known to occasionally be the source of anophthalmia. The deletion of this region of chromosome has also been associated with patients having a small tongue, and high arched palate, developmental and growth retardation, undescended testes with a micropenis, and hypothyroidism. The region that has been deleted is region q22.1-q22.3. This confirms that region 22 on chromosome 14 influences the development of the eye.

Colobomas can be associated with a mutation in the "PAX2" gene.

Eye abnormalities have been shown to occur in over 90% of children with fetal alcohol syndrome.

The most extensive epidemiological survey on this congenital malformation has been carried out by Dharmasena et al and using English National Hospital Episode Statistics, they calculated the annual incidence of anophthalmia, microphthalmia and congenital malformations of orbit/lacrimal apparatus from 1999 to 2011. According to this study the annual incidence of congenital microphthalmia in the United Kingdom was 10.8 (8.2 to 13.5) in 1999 and 10.0 (7.6 to 12.4) in 2011.

It is known to occur in Scotch Collies (smooth and rough collies), Shetland Sheepdogs, Australian Shepherds, Border Collies, Lancashire Heelers, and Nova Scotia Duck Tolling Retrievers. Frequency is high in Collies and Shetland Sheepdogs, and low in Border Collies and NSDTRs. In the United States, incidence in the genotype of collies has been estimated to be as high as 95 percent, with a phenotypic incidence of 80 to 85 percent.

Hypertropia may be either congenital or acquired, and misalignment is due to imbalance in extraocular muscle function. The superior rectus, inferior rectus, superior oblique, and inferior oblique muscles affect the vertical movement of the eyes. These muscles may be either paretic, restrictive (fibrosis) or overactive effect of the muscles. Congenital cases may have developmental abnormality due to abnormal muscle structure, usually muscle atrophy / hypertrophy or rarely, absence of the muscle and incorrect placement.

Specific & common causes include:

- Superior oblique Palsy / Congenital fourth nerve palsy

- Inferior oblique overaction

- Brown's syndrome

- Duane's retraction syndrome

- Double elevator palsy

- Fibrosis of rectus muscle in Graves Disease (most commonly inferior rectus is involved)

- Surgical trauma to the vertical muscles (e.g. during scleral buckling surgery or cataract surgery causing iatrogenic trauma to the vertical muscles).

Sudden onset hypertropia in a middle aged or elderly adult may be due to compression of the trochlear nerve and mass effect from a tumor, requiring urgent brain imaging using MRI to localise any space occupying lesion. It could also be due to infarction of blood vessels supplying the nerve, due to diabetes and atherosclerosis. In other instances it may be due to an abnormality of neuromuscular transmission, i.e., Myasthenia Gravis.

CEA is caused by improper development of the eye. Failure of the cells of the posterior portion of the optic vesicles to express growth hormone affects the differentiation of other cells of the eye. The choroid, especially lateral to the optic disc, is hypoplastic (underdeveloped). A coloboma, or hole, may form in or near the optic disc due to a failed closure of embryonic tissue. The degree of these abnormalities varies between individual dogs, and even between the same dog's eyes. CEA is inherited as an autosomal recessive trait that has a penetrance reaching 100 percent, and has been localized to canine chromosome 37.

Optic pits occur equally between men and women. They are seen in roughly 1 in 10,000 eyes, and approximately 85% of optic pits are found to be unilateral (i.e. in only one eye of any affected individual). About 70% are found on the temporal side (or lateral one-half) of the optic disc. Another 20% are found centrally, while the remaining pits are located either superiorly (in the upper one-half), inferiorly (in the lower one-half), or nasally (in the medial one-half towards the nose).

No particular risk factors have been conclusively identified; however, there have been a few reports that demonstrate an autosomal dominant pattern of inheritance in some families. Therefore, a family history of optic pits may be a possible risk factor.

This remains undetermined at the present time. A recent study by Major et al. reports that:

"Prematurity, family history or secondary ocular history, perinatal or gestational complications, systemic disorders, use of supplemental oxygen as a neonate, use of systemic medications, and male sex were found to be significant risk factors for infantile esotropia."

Further recent evidence indicates that a cause for "infantile strabismus" may lie with the input that is provided to the visual cortex. In particular, neonates who suffer injuries that, directly or indirectly, perturb binocular inputs into the primary visual cortex (V1) have a far higher risk of developing strabismus than other infants.

A paper published by Eltern für Impfaufklärung, a German Anti-Vaccination activist group, cites a study by The Robert Koch Institute (RKI), claiming significant correlation between children who received Vaccinations and the onset of cause of Spine, Face & Eye Asymmetry.

Refractive errors such as hyperopia and Anisometropia may be associated abnormalities found in patients with vertical strabismus.

The vertical miscoordination between the two eyes may lead to

- Strabismic amblyopia, (due to deprivation / suppression of the deviating eye)

- cosmetic defect (most noticed by parents of a young child and in photographs)

- Face turn, depending on presence of binocular vision in a particular gaze

- diplopia or double vision - more seen in adults (maturity / plasticity of neural pathways) and suppression mechanisms of the brain in sorting out the images from the two eyes.

- cyclotropia, a cyclotorsional deviation of the eyes (rotation around the visual axis), particularly when the root cause is an oblique muscle paresis causing the hypertropia.

Although many perinatal and prenatal risk factors for ONH have been suggested, the predominant, enduring, most frequent risk factors are young maternal age and primiparity (the affected child being the first child born to the mother). Increased frequency of delivery by caesarean section and fetal/neonatal complications, preterm labor, gestational vaginal bleeding, low maternal weight gain, and weight loss during pregnancy are also associated with ONH.

Optic nerve hypoplasia (ONH) is a congenital condition in which the optic nerve is underdeveloped (small).

Many times, de Morsier’s Syndrome or septo-optic dysplasia (SOD) is associated with ONH, however, it is possible to have ONH without any additional issues like SOD. SOD is a condition that can involve multiple problems in the midline structures of the brain, stemming from miswiring of the brain and central nervous system. Besides having small optic nerves, persons with ONH can have agenesis of the corpus callosum, absence of the septum pellucidum, maldevelopment of the anterior and posterior pituitary gland, and anomalies of the hypothalamus. Because of this, all children with ONH are at risk for developmental delays and hormonal deficiencies, regardless of severity of ONH, or whether abnormalities are visible by MRI.

ONH is the single leading cause of permanent legal blindness in children in the western world. The incidence of ONH is increasing, although it is difficult to estimate the true prevalence. Between 1980 and 1999, the occurrences of ONH in Sweden increased four-fold to 7.2 per 100,000, while all other causes of childhood blindness had declined. In 1997, ONH overtook retinopathy of prematurity as the single leading cause of infant blindness in Sweden, with 6.3 in every 100,000 births diagnosed with ONH. The most recent prevalence report out of England in 2006 is 10.9 per 100,000.

Most patients are diagnosed by the age of 10 years and Duane's is more common in girls (60 percent of the cases) than boys (40 percent of the cases). A French study reports that this syndrome accounts for 1.9% of the population of strabismic patients, 53.5% of patients are female, is unilateral in 78% of cases, and the left eye (71.9%) is affected more frequently than the right. Around 10–20% of cases are familial; these are more likely to be bilateral than non-familial Duane syndrome. Duane syndrome has no particular race predilection.

Between 2 and 5% of the population in western countries have amblyopia. In the U.K., 90% of visual health appointments in the child are concerning amblyopia.

Depending on the chosen criterion for diagnosis, between 1 and 4% of the children have amblyopia.

Untreated glaucoma leads to total blindness. Surgical treatment is required. Presently-utilized surgical procedures include goniotomy, trabeculotomy, or trabeculectomy.

The presence of a small eye within the orbit can be a normal incidental finding but in most cases it is abnormal and results in blindness. The incidence is 14 per 100,000 and the condition affects 3-11% of blind children.

Buphthalmos (plural: buphthalmoses) is enlargement of the eyeball and is most commonly seen in infants and young children. It is sometimes referred to as buphthalmia (plural buphthalmias). It usually appears in the newborn period or the first 3 months of life. and in most cases indicates the presence of congenital (infantile) glaucoma, which is a disorder in which elevated pressures within the eye lead to structural eye damage and vision loss.

Causes of photophobia relating directly to the eye itself include:

- Achromatopsia

- Aniridia

- Anticholinergic drugs may cause photophobia by paralyzing the iris sphincter muscle.

- Aphakia (absence of the lens of the eye)

- Blepharitis

- Buphthalmos (abnormally narrow angle between the cornea and iris)

- Cataracts

- Coloboma

- Cone dystrophy

- Congenital abnormalities of the eye

- Viral conjunctivitis ("pink eye")

- Corneal abrasion

- Corneal dystrophy

- Corneal ulcer

- Disruption of the corneal epithelium, such as that caused by a corneal foreign body or keratitis

- Ectopia lentis

- Endophthalmitis

- Eye trauma caused by disease, injury, or infection such as chalazion, episcleritis, glaucoma, keratoconus, or optic nerve hypoplasia

- Hydrophthalmos, or congenital glaucoma

- Iritis

- The drug isotretinoin (Accutane/Roaccutane) has been associated with photophobia

- Optic neuritis

- Pigment dispersion syndrome

- Pupillary dilation (naturally or chemically induced)

- Retinal detachment

- Scarring of the cornea or sclera

- Uveitis

Infantile esotropia is an ocular condition of early onset in which one or either eye turns inward. It is a specific sub-type of esotropia and has been a subject of much debate amongst ophthalmologists with regard to its naming, diagnostic features, and treatment.

The gene sal-like 4 (SALL4) or CHN1 ("chimerin") has became a mutated gene (protein) and it is also one of the cause of the body's Duane Syndrome.

Keratoconjunctivitis sicca is relatively common within the United States, especially so in older patients. Specifically, the persons most likely to be affected by dry eyes are those aged 40 or older. 10-20% of adults experience Keratoconjunctivitis sicca. Approximately 1 to 4 million adults (age 65-84) in the USA are effected.

While persons with autoimmune diseases have a high likelihood of having dry eyes, most persons with dry eyes do not have an autoimmune disease. Instances of Sjögren syndrome and keratoconjunctivitis sicca associated with it are present much more commonly in women, with a ratio of 9:1. In addition, milder forms of keratoconjunctivitis sicca also are more common in women. This is partly because hormonal changes, such as those that occur in pregnancy, menstruation, and menopause, can decrease tear production.

In areas of the world where malnutrition is common, vitamin A deficiency is a common cause. This is rare in the United States.

Racial predilections do not exist for this disease.

Neurological causes for photophobia include:

- Autism spectrum disorders

- Chiari malformation

- Occipital Neuralgia

- Dyslexia

- Encephalitis including Myalgic encephalomyelitis aka Chronic fatigue syndrome

- Meningitis

- Trigeminal disturbance causes central sensitization (hence, multiple other associated hypersensitivities. Causes can be bad bite, infected tooth, etc.

- Subarachnoid haemorrhage

- Tumor of the posterior cranial fossa

Sclerocornea is a congenital anomaly of the eye in which the cornea blends with sclera, having no clear-cut boundary. The extent of the resulting opacity varies from peripheral to total ("sclerocornea totalis"). The severe form is thought to be inherited in an autosomal recessive manner, but there may be another, milder form that is expressed in a dominant fashion. In some cases the patients also have abnormalities beyond the eye (systemic), such as limb deformities and craniofacial and genitourinary defects.

According to one tissue analysis performed after corneal transplantation, the sulfation pattern of keratan sulfate proteoglycans in the affected area is typical for corneal rather than scleral tissue.

Sclerocornea may be concurrent with cornea plana.