The effects a coloboma has on the vision can be mild or more severe depending on the size and location of the gap. If, for example, only a small part of the iris is missing, vision may be normal, whereas if a large part of the retina or optic nerve is missing, vision may be poor and a large part of the visual field may be missing. This is more likely to cause problems with mobility if the lower visual field is absent. Other conditions can be associated with a coloboma. Sometimes, the eye may be reduced in size, a condition called microphthalmia. Glaucoma, nystagmus, scotoma, or strabismus may also occur.

Other ocular malformations that include coloboma or are related to it:

- CHARGE syndrome, a term that came into use as an acronym for the set of unusual congenital features seen in a number of newborn children. The letters stand for: coloboma of the eye, heart defects, atresia of the nasal choanae, retardation of growth and/or development, genital and/or urinary abnormalities, and ear abnormalities and deafness. Although these features are no longer used in making a diagnosis, the name has remained.

- Cat eye syndrome, caused by the short arm (p) and a small section of the long arm (q) of human chromosome 22 being present three (trisomic) or four times (tetrasomic) instead of the usual two times. The term "cat eye" was coined because of the particular appearance of the vertical colobomas in the eyes of some patients.

- Patau syndrome (trisomy 13), a chromosomal abnormality that can cause a number of deformities, some of which include structural eye defects, including microphthalmia, Peters anomaly, cataract, iris and/or fundus coloboma, retinal dysplasia or retinal detachment, sensory nystagmus, cortical visual loss, and optic nerve hypoplasia.

- Treacher Collins syndrome, autosomal dominant syndrome caused by mutation of "TCOF1". Coloboma is part of a set of characteristic facies that features craniofacial malformations, such as downslanting eyes, ear anomalies, or hypoplasia of zygomatic bone and jaw (micrognathia).

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.

The primary vitreous used in formation of the eye during fetal development remains in the eye upon birth and is hazy and scarred. The symptoms are leukocoria, strabismus, nystagmus and blurred vision, blindness.

Microphthalmia (Greek: μικρός "micros" = small; ὀφθαλμός "ophthalmos" = eye), also referred as microphthalmos, is a developmental disorder of the eye in which one (unilateral microphthalmia) or both (bilateral microphthalmia) eyes are abnormally small and have anatomic malformations. It is different from nanophthalmos in which the eye is small in size but has no anatomical alterations.

Vision in the affected eye is impaired, the degree of which depends on the size of the defect, and typically affects the visual field more than visual acuity. Additionally, there is an increased risk of serous retinal detachment, manifesting in 1/3 of patients. If retinal detachment does occur, it is usually not correctable and all sight is lost in the affected area of the eye, which may or may not involve the macula.

Buphthalmos in itself is merely a clinical sign and does not generate symptoms. Patients with glaucoma often initially have no symptoms; later, they can exhibit excessive tearing (lacrimation) and extreme sensitivity to light (photophobia). On ophthalmologic exam, one can detect increased intraocular pressure, distortion of the optic disc, and corneal edema, which manifests as haziness.

Other symptoms include a prominent eyeball, Haab's striae in the Descemet's membrane of the cornea, an enlarged cornea, and myopia.

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.

Causes a ‘white reflex’ in the affected eye (leukocoria), prompting further investigation.

Hypertropia is a condition of misalignment of the eyes (strabismus), whereby the visual axis of one eye is higher than the fellow fixating eye.

Hypotropia is the similar condition, focus being on the eye with the visual axis lower than the fellow fixating eye.

Dissociated Vertical Deviation is a special type of hypertropia leading to slow upward drift of one or rarely both eyes, usually when the patient is inattentive.

Anisocoria is a condition characterized by an unequal size of the eyes' pupils. Affecting 20% of the population, it can be an entirely harmless condition or a symptom of more serious medical problems.

Aniridia is the absence of the iris, usually involving both eyes. It can be congenital or caused by a penetrant injury. Isolated aniridia is a congenital disorder which is not limited to a defect in iris development, but is a panocular condition with macular and optic nerve hypoplasia, cataract, and corneal changes. Vision may be severely compromised and the disorder is frequently associated with a number of ocular complications: nystagmus, amblyopia, buphthalmos, and cataract. Aniridia in some individuals occurs as part of a syndrome, such as WAGR syndrome (kidney nephroblastoma (Wilms tumour), genitourinary anomalies and intellectual disability), or Gillespie syndrome (cerebellar ataxia).

Infantile glaucoma, which often produces the clinical sign of buphthalmos, can be caused when an abnormally narrow angle between the cornea and iris blocks the outflow of aqueous humor; this causes increased intraocular pressure and eventual enlargement of the globe (eyeball). Angle closure can be caused by developmental abnormalities of the eye as well as the presence of abnormal structures within the vitreous.

Anisocoria is a common condition, defined by a difference of 0.4 mm or more between the sizes of the pupils of the eyes.

Anisocoria has various causes:

- Physiological anisocoria: About 20% of normal people have a slight difference in pupil size which is known as physiological anisocoria. In this condition, the difference between pupils is usually less than 1 mm.

- Horner's syndrome

- Mechanical anisocoria: Occasionally previous trauma, eye surgery, or inflammation (uveitis, angle closure glaucoma) can lead to adhesions between the iris and the lens.

- Adie tonic pupil: Tonic pupil is usually an isolated benign entity, presenting in young women. It may be associated with loss of deep tendon reflex (Adie's syndrome). Tonic pupil is characterized by delayed dilation of iris especially after near stimulus, segmental iris constriction, and sensitivity of pupil to a weak solution of pilocarpine.

- Oculomotor nerve palsy: Ischemia, intracranial aneurysm, demyelinating diseases (e.g., multiple sclerosis), head trauma, and brain tumors are the most common causes of oculomotor nerve palsy in adults. In ischemic lesions of the oculomotor nerve, pupillary function is usually spared whereas in compressive lesions the pupil is involved.

- Pharmacological agents with anticholinergic or sympathomimetic properties will cause anisocoria, particularly if instilled in one eye. Some examples of pharmacological agents which may affect the pupils include pilocarpine, cocaine, tropicamide, MDMA, dextromethorphan, and ergolines. Alkaloids present in plants of the genera "Brugmansia" and "Datura", such as scopolamine, may also induce anisocoria.

- Migraines

Coloboma of optic nerve, is a rare defect of the optic nerve that causes moderate to severe visual field defects.

Coloboma of the optic nerve is a congenital anomaly of the optic disc in which there is a defect of the inferior aspect of the optic nerve. The issue stems from incomplete closure of the embryonic fissure while in utero. A varying amount of glial tissue typically fills the defect, manifests as a white mass.

More than 70% of children with ONH experience developmental delay, ranging from isolated focal defects to delay in all areas of development (global delay). Motor delay is most common (75%) and communication delay is least common (44%). Predictors of significantly delayed development include hypoplasia or agenesis of the corpus callosum and hypothyroidism. The absence of the septum pellucidum does not predict developmental delay. Delays may occur in unilateral (39%) as well as bilateral (78%) cases.

Aniridia may be broadly divided into hereditary and sporadic forms. Hereditary aniridia is usually transmitted in an autosomal dominant manner (each offspring has a 50% chance of being affected), although rare autosomal recessive forms (such as Gillespie syndrome) have also been reported. Sporadic aniridia mutations may affect the WT1 region adjacent to the AN2 aniridia region, causing a kidney cancer called nephroblastoma (Wilms tumor). These patients often also have genitourinary abnormalities and intellectual disability (WAGR syndrome).

Several different mutations may affect the PAX6 gene. Some mutations appear to inhibit gene function more than others, with subsequent variability in the severity of the disease. Thus, some aniridic individuals are only missing a relatively small amount of iris, do not have foveal hypoplasia, and retain relatively normal vision. Presumably, the genetic defect in these individuals causes less "heterozygous insufficiency," meaning they retain enough gene function to yield a milder phenotype.

- AN

- Aniridia and absent patella

- Aniridia, microcornea, and spontaneously reabsorbed cataract

- Aniridia, cerebellar ataxia, and mental deficiency (Gillespie syndrome)

Cherry eye is a disorder of the nictitating membrane (NM), also called the third eyelid, present in the eyes of dogs and cats. Cherry eye is most often seen in young dogs under the age of two. Common misnomers include adenitis, hyperplasia, adenoma of the gland of the third eyelid; however, cherry eye is not caused by hyperplasia, neoplasia, or primary inflammation. In many species, the third eyelid plays an essential role in vision by supplying oxygen and nutrients to the eye via tear production. Normally, the gland can evert without detachment. Cherry eye results from a defect in the retinaculum which is responsible for anchoring the gland to the periorbita. This defect causes the gland to prolapse and protrude from the eye as a red fleshy mass. Problems arise as sensitive tissue dries out and is subjected to external trauma Exposure of the tissue often results in secondary inflammation, swelling, or infection. If left untreated, this condition can lead to Keratoconjunctivitis sicca (KCS) and other complications.

ONH can be unilateral (in one eye) or bilateral (in both eyes), although it presents most often bilaterally (80%). Because the unilateral cases tend to have better vision, they are typically diagnosed at a later age than those with bilateral ONH. Visual acuity can range from no light perception to near-normal vision.

Children diagnosed with ONH generally present with vision problems which include nystagmus (involuntary movement of the eyes), which tends to develop at 1 to 3 months and/or strabismus (inability to align both eyes simultaneously), manifested during the first year of life.

The majority of children affected experience improvement in vision during the first few years of life, though the reason for this occurrence is unknown. There have been no reported cases of decline in vision due to ONH.

Cherry eye is most common in young dogs, especially breeds such as Cavalier King Charles Spaniel, English Bulldog, Lhasa Apso, Shih Tzu, West Highland White Terrier, Pug, Bloodhound, American Cocker Spaniel, and Boston Terrier Cherry eye is rare in felines, but can occur. This defect is most common in the Burmese breed of felines. A similar condition exists in dwarf lop-eared rabbits, which occurs in the harderian gland. Similar surgical treatment is necessary.

Cherry eye is not considered a genetic problem, as no proof of inheritance has been determined. The NM contains many glands which merge and appear as a single gland. Typically, glands secrete tears for lubrication of the cornea. Lack of anchoring allows the gland to flip up, causing the gland to prolapse.

Symptoms include a visible fleshy mass, abnormal tear production, and a discharge or drainage from the eye. Cherry eye is typically diagnosed by examination of the conjunctiva and nictitating membrane. The most obvious symptom of cherry eye is a round fleshy mass through medial canthus of the eye, similar in appearance to the fruit it is named for. This mass may be unilateral or ‘’bilateral’’. Both eyes may develop cherry eye at different times in the animal’s life. Other symptoms of cherry eye include drainage from the eye and abnormal tear production. Initially, cherry eye results in overproduction of tears, but eventually changes to unsubstantial tear production.

Monofixation syndrome (MFS) (also: microtropia or microstrabismus) is an eye condition defined by less-than-perfect binocular vision. It is defined by a small angle deviation with suppression of the deviated eye and the presence of binocular peripheral fusion. That is, MFS implies peripheral fusion without central fusion.

Aside the manifest small-angle deviation ("tropia"), subjects with MFS often also have a large-angle latent deviation ("phoria"). Their stereoacuity is often in the range of 3000 to 70 arcsecond, and a small central suppression scotoma of 2 to 5 deg.

A rare condition, MFS is estimated to affect only 1% of the general population. There are three distinguishable forms of this condition: primary constant, primary decompensating, and consecutive MFS. It is believed that primary MFS is a result of a primary sensorial defect, predisposing to anomalous retinal correspondence.

Secondary MFS is a frequent outcome of surgical treatment of congenital esotropia. A study of 1981 showed MFS to result in the vast majority of cases if surgical alignment is reached before the age of 24 months and only in a minority of cases if it is reached later.

MFS was first described by Marshall Parks.

Cyclopia (also cyclocephaly or synophthalmia) is a rare form of holoprosencephaly and is a congenital disorder (birth defect) characterized by the failure of the embryonic prosencephalon to properly divide the orbits of the eye into two cavities. Its incidence is 1 in 16,000 in born animals and 1 in 200 in miscarried fetuses.

Relative afferent pupillary defect (RAPD) or Marcus Gunn pupil is a medical sign observed during the swinging-flashlight test whereupon the patient's pupils constrict less (therefore appearing to dilate) when a bright light is swung from the unaffected eye to the affected eye. The affected eye still senses the light and produces pupillary sphincter constriction to some degree, albeit reduced.

The most common cause of Marcus Gunn pupil is a lesion of the optic nerve (between the retina and the optic chiasm) or severe retinal disease. It is named after Scottish ophthalmologist Robert Marcus Gunn.

A second common cause of Marcus Gunn pupil is a contralateral optic tract lesion, due to the different contributions of the intact nasal and temporal hemifields.

The Marcus Gunn pupil is a relative afferent pupillary defect indicating a decreased pupillary response to light in the affected eye.

In the swinging flashlight test, a light is alternately shone into the left and right eyes. A normal response would be equal constriction of both pupils, regardless of which eye the light is directed at. This indicates an intact direct and consensual pupillary light reflex. When the test is performed in an eye with an afferent pupillary defect, light directed in the affected eye will cause only mild constriction of both pupils (due to decreased response to light from the afferent defect), while light in the unaffected eye will cause a normal constriction of both pupils (due to an intact efferent path, and an intact consensual pupillary reflex). Thus, light shone in the affected eye will produce less pupillary constriction than light shone in the unaffected eye.

A Marcus Gunn pupil is distinguished from a total CN II lesion, in which the affected eye perceives "no" light. In that case, shining the light in the affected eye produces no effect.

Anisocoria is absent. A Marcus Gunn pupil is seen, among other conditions, in optic neuritis. It is also common in retrobulbar optic neuritis due to multiple sclerosis but only for 3–4 weeks, until the visual acuity begins to improve in 1–2 weeks and may return to normal.

Typically, the nose is either missing or replaced with a non-functional nose. This deformity (called proboscis) usually forms above the center eye or on the back, and is characteristic of a form of cyclopia called rhinencephaly or rhinocephaly. Most such embryos are either naturally aborted or are stillborn upon delivery.

Although cyclopia is rare, several cyclopic human babies are preserved in medical museums (e.g. The Vrolik Museum, Amsterdam, Trivandrum Medical College).

Some extreme cases of cyclopia have been documented in farm animals (horses, sheep, pigs, and sometimes chickens). In such cases, the nose and mouth fail to form, or the nose grows from the roof of the mouth obstructing airflow, resulting in suffocation shortly after birth.