Heterochromia is classified primarily by onset: as either genetic or acquired.

Although a distinction is frequently made between heterochromia that affects an eye completely or only partially (segmental heterochromia), it is often classified as either genetic (due to mosaicism or congenital) or acquired, with mention as to whether the affected iris or portion of the iris is darker or lighter. Most cases of heterochromia are hereditary, caused by certain diseases and syndromes. Sometimes one eye may change color following disease or injury.

Acquired heterochromia is usually due to injury, inflammation, the use of certain eyedrops that damages the iris, or tumors.

An odd-eyed cat is a cat with one blue eye and one eye either green, yellow, or brown. This is a feline form of complete heterochromia, a condition that occurs in some other animals. The condition most commonly affects white-colored cats, but may be found in a cat of any color, provided that it possesses the white spotting gene.

In flash photographs, odd-eyed cats typically show a red-eye effect in the blue eye, but not in the other eye. This is due to the combined effect of the (normal) presence of a tapetum lucidum in both eyes and the absence of melanin in the blue eye. The tapetum lucidum produces eyeshine in both eyes, but in the non-blue eye a layer of melanin over the tapetum lucidum selectively removes some colors of light.

This condition is usually unilateral, and its symptoms vary from none to mild blurring and discomfort. Signs include diffuse iris atrophy and small white keratic precipitates (deposits on the inner surface of the cornea), cells presenting in the anterior chamber as well as the anterior vitreous. Glaucoma and cataract occur frequently.

Fuchs heterochromic iridocyclitis (FHI) is a chronic unilateral uveitis appearing with the triad of heterochromia, predisposition to cataract and glaucoma, and keratitic precipitates on the posterior corneal surface. Patients are often asymptomatic and the disease is often discovered through investigation of the cause of the heterochromia or cataract. Neovascularisation (growth of new abnormal vessels) is possible and any eye surgery, such as cataract surgery, can cause bleeding from the fragile vessels in the atrophic iris causing accumulation of blood in anterior chamber of the eye, also known as hyphema.

Traction caused by VMA is the underlying pathology of an eye disease called symptomatic VMA. There is evidence that symptomatic VMA can contribute to the development of several well-known eye disorders, such as macular hole and macular pucker, that can cause visual impairment, including blindness. It may also be associated with age-related macular degeneration (AMD), diabetic macular edema (DME), retinal vein occlusion, and diabetic retinopathy (DR).

The characteristic features of the syndrome are:

- Limitation of abduction (outward movement) of the affected eye.

- Less marked limitation of adduction (inward movement) of the same eye.

- Retraction of the eyeball into the socket on adduction, with associated narrowing of the palpebral fissure (eye closing).

- Widening of the palpebral fissure on attempted abduction. (N. B. Mein and Trimble point out that this is "probably of no significance" as the phenomenon also occurs in other conditions in which abduction is limited.)

- Poor convergence.

- A head turn to the side of the affected eye to compensate for the movement limitations of the eye(s) and to maintain binocular vision.

While usually isolated to the eye abnormalities, Duane syndrome can be associated with other problems including cervical spine abnormalities Klippel-Feil syndrome, Goldenhar syndrome, heterochromia, and congenital deafness.

In the clinical setting, the principal difficulties in differential diagnosis arise as a consequence of the very early age at which patients with this condition first present. The clinician must be persistent in examining abduction and adduction, and in looking for any associated palpebral fissure changes or head postures, when attempting to determine whether what often presents as a common childhood squint (note-"squint" is a British term for two eyes not looking in the same direction) is in fact Duane syndrome. Fissure changes, and the other associated characteristics of Duane's such as up or down shoots and globe retraction, are also vital when deciding whether any abduction limitation is the result of Duane's and not a consequence of VI or abducens cranial nerve palsy.

Acquired Duane's syndrome is a rare event occurring after peripheral nerve palsy.

Reis-Bücklers corneal dystrophy, also known as corneal dystrophy of Bowman layer, type I, is a rare, corneal dystrophy of unknown cause, in which the Bowman's layer of the cornea undergoes disintegration. The disorder is inherited in an autosomal dominant fashion, and is associated with mutations in the gene TGFB1.

Reis-Bücklers dystrophy causes a cloudiness in the corneas of both eyes, which may occur as early as 1 year of age, but usually develops by 4 to 5 years of age. It is usually evident within the first decade of life. This cloudiness, or opacity, causes the corneal epithelium to become elevated, which leads to corneal opacities. The corneal erosions may prompt attacks of redness and swelling in the eye (ocular hyperemia), eye pain, and photophobia. Significant vision loss may occur.

Reis-Bücklers dystrophy is diagnosed by clinical history physical examination of the eye. Labs and imaging studies are not necessary. Treatment may include a complete or partial corneal transplant, or photorefractive keratectomy.

Vitreomacular adhesion (VMA) is a human medical condition where the vitreous gel (or simply vitreous) of the human eye adheres to the retina in an abnormally strong manner. As the eye ages, it is common for the vitreous to separate from the retina. But if this separation is not complete, i.e. there is still an adhesion, this can create pulling forces on the retina that may result in subsequent loss or distortion of vision. The adhesion in of itself is not dangerous, but the resulting pathological vitreomacular traction (VMT) can cause severe ocular damage.

The current standard of care for treating these adhesions is pars plana vitrectomy (PPV), which involves surgically removing the vitreous from the eye. A biological agent for non-invasive treatment of adhesions called ocriplasmin has been approved by the FDA on Oct 17 2012.

Patients with Reis-Bücklers dystrophy develop a reticular pattern of cloudiness in the cornea. This cloudiness, or opacity, usually appears in both eyes (bilaterally) in the upper cornea by 4 or 5 years of age. The opacity elevates the corneal epithelium, eventually leading to corneal erosions that prompt attacks of ocular hyperemia, pain, and photophobia. These recurrent painful corneal epithelial erosions often begin as early as 1 year of age.

With time, the corneal changes progress into opacities in Bowman's membrane, which gradually becomes more irregular and more dense. Significant vision loss may occur. However, vascularization of the cornea is not present.

The X-linked varieties of congenital stationary night blindness (CSNB) can be differentiated from the autosomal forms by the presence of myopia, which is typically absent in the autosomal forms. Patients with CSNB often have impaired night vision, myopia, reduced visual acuity, strabismus, and nystagmus. Individuals with the complete form of CSNB (CSNB1) have highly impaired rod sensitivity (reduced ~300x) as well as cone dysfunction. Patients with the incomplete form can present with either myopia or hyperopia.

Cryptophthalmos is a rare congenital anomaly in which the skin is continuous over the eyeball with absence of eyelids. It is classified into three types: complete, incomplete and abortive. Failure of eyelid separation can be associated with maldevelopment of the underlying cornea and microphthalmia. Cryptophthalmos usually occurs on both sides and occurs in association with other multiple malformations collectively referred to as Fraser syndrome.

X-linked congenital stationary night blindness (CSNB) is a rare X-linked non-progressive retinal disorder. It has two forms, complete, also known as type-1 (CSNB1), and incomplete, also known as type-2 (CSNB2), depending on severity. In the complete form (CSNB1), there is no measurable rod cell response to light, whereas this response is measurable in the incomplete form. Patients with this disorder have difficulty adapting to low light situations due to impaired photoreceptor transmission. These patients also often have reduced visual acuity, myopia, nystagmus, and strabismus. CSNB1 is caused by mutations in the gene NYX, which encodes a protein involved in retinal synapse formation or synaptic transmission. CSNB2 is caused by mutations in the gene CACNA1F, which encodes a voltage-gated calcium channel Ca1.4.

Not all Congenital Stationary Night Blindness (CSNB) are inherited in X-linked pattern. There are also dominant and recessive inheritance patterns for CSNB.

Hyphema (or hyphaema, see spelling differences) is blood in the front (anterior) chamber of the eye. It may appear as a reddish tinge, or it may appear as a small pool of blood at the bottom of the iris or in the cornea.

Hyphemas are frequently caused by injury, and may partially or completely block vision. The most common causes of hyphema are intraocular surgery, blunt trauma, and lacerating trauma. Hyphemas may also occur spontaneously, without any inciting trauma. Spontaneous hyphemas are usually caused by the abnormal growth of blood vessels (neovascularization), tumors of the eye (retinoblastoma or iris melanoma), uveitis, or vascular anomalies (juvenile xanthogranuloma). Additional causes of spontaneous hyphema include: rubeosis iridis, myotonic dystrophy, leukemia, hemophilia, and von Willebrand disease. Conditions or medications that cause thinning of the blood, such as aspirin, warfarin, or drinking alcohol may also cause hyphema.

Symptoms vary from one type of the syndrome to another and from one patient to another, but they include:

- Very pale or brilliantly blue eyes, eyes of two different colors (complete heterochromia), or eyes with one iris having two different colors (sectoral heterochromia)

- A forelock of white hair ("poliosis"), or premature graying of the hair

- Appearance of wide-set eyes due to a prominent, broad nasal root ("dystopia canthorum")—particularly associated with Type I) also known as "telecanthus"

- Moderate to profound hearing loss (higher frequency associated with Type II);

- A low hairline and eyebrows that meet in the middle ("synophrys")

- Patches of white skin pigmentation, in some cases

- Abnormalities of the arms, associated with Type III

- neurologic manifestations, associated with Type IV

- Cleft lip, mostly associated with Type I

Waardenburg syndrome has also been associated with a variety of other congenital disorders, such as intestinal and spinal defects, elevation of the scapula and cleft lip and palate. Sometimes this is concurrent with Hirschsprung disease.

Signs that are found in patients on the affected side of the face include

- partial ptosis

- upside-down ptosis (slight elevation of the lower lid)

- anhidrosis

- miosis

- pseudoenophthalmos (the impression that the eye is sunken, caused by a narrow palpebral aperture)

- pupillary dilation lag

- loss of ciliospinal reflex

- bloodshot conjunctiva, depending on the site of lesion.

- unilateral straight hair (in congenital Horner's syndrome); the hair on the affected side may be straight in some cases.

- heterochromia iridum (in congenital Horner's syndrome)

Interruption of sympathetic pathways leads to several implications. It inactivates the dilator muscle and thereby produces miosis. It inactivates the superior tarsal muscle which produces ptosis. It inactivates the orbitalis muscle which produces the effect of enophthalmos. It also reduces sweat secretion in the face.

Sometimes there is flushing on the affected side of the face due to dilation of blood vessels under the skin. The pupil's light reflex is maintained as this is controlled via the parasympathetic nervous system.

In children, Horner's syndrome sometimes leads to heterochromia, a difference in eye color between the two eyes. This happens because a lack of sympathetic stimulation in childhood interferes with melanin pigmentation of the melanocytes in the superficial stroma of the iris.

In veterinary medicine, signs can include partial closure of the third eyelid, or nictitating membrane.

Horner's syndrome is a combination of symptoms that arises when a group of nerves known as the sympathetic trunk is damaged. The signs and symptoms occur on the same side as the lesion of the sympathetic trunk. It is characterized by miosis (a constricted pupil), partial ptosis (a weak, droopy eyelid), apparent anhidrosis (decreased sweating), with or without enophthalmos (inset eyeball).

The nerves of the sympathetic trunk arise from the spinal cord in the chest, and from there ascend to the neck and face. The nerves are part of the sympathetic nervous system, a division of the autonomic (or involuntary) nervous system. Once the syndrome has been recognized, medical imaging and response to particular eye drops may be required to identify the location of the problem and the underlying cause.

Piebaldism is a rare autosomal dominant disorder of melanocyte development. Common characteristics include a congenital white forelock, scattered normal pigmented and hypopigmented macules and a triangular shaped depigmented patch on the forehead. There is nevertheless great variation in the degree and pattern of presentation, even within affected families. In some cases, piebaldism occurs together with severe developmental problems, as in Waardenburg syndrome and Hirschsprung's disease. It has been documented to occur in all races; early photographers captured many images of African piebalds used as a form of amusement, and George Catlin is believed to have painted several portraits of Native Americans of the Mandan tribe who were affected by piebaldism. Piebaldism is found in nearly every species of mammal. It is very common in mice, rabbits, dogs, sheep, deer, cattle and horses—where selective breeding has increased the incidence of the mutation-, but occurs among chimpanzees and other primates only as rarely as among humans. Piebaldism is completely unrelated to acquired or infectious conditions such as vitiligo or poliosis.

"Pie" is a word for multi-colored and "bald" is related to a root word for "skin." Although piebaldism may visually appear to be partial albinism, it is a fundamentally different condition. The vision problems associated with albinism are not usually present as eye pigmentation is normal. Piebaldism differs from albinism in that the affected cells maintain the ability to produce pigment but have that specific function turned off. In albinism the cells lack the ability to produce pigment altogether. Human piebaldism has been observed to be associated with a very wide range and varying degrees of endocrine disorders, and is occasionally found together with heterochromia of the irises, congenital deafness, or incomplete gastrointestinal tract development, possibly all with the common cause of premature cutting off of human fetal growth hormone during gestation. Piebaldism is a kind of neurocristopathy, involving defects of various neural crest cell lineages that include melanocytes, but also involving many other tissues derived from the neural crest. Oncogenic factors, including mistranscription, are hypothesized to be related to the degree of phenotypic variation among affected individuals.

Waardenburg syndrome is a rare genetic disorder most often characterized by varying degrees of deafness, minor defects in structures arising from the neural crest, and pigmentation changes. It was first described in 1951. The syndrome was later found to have four types. For example, type II was identified in 1971, to describe cases where dystopia canthorum was not present. Some types are now split into subtypes, based upon the gene responsible for the condition.

Sturge–Weber syndrome is usually manifested at birth by a port-wine stain on the forehead and upper eyelid of one side of the face, or the whole face. The birthmark can vary in color from light pink to deep purple and is caused by an overabundance of capillaries around the ophthalmic branch of the trigeminal nerve, just under the surface of the face. There is also malformation of blood vessels in the pia mater overlying the brain on the same side of the head as the birthmark. This causes calcification of tissue and loss of nerve cells in the cerebral cortex.

Neurological symptoms include seizures that begin in infancy and may worsen with age. Convulsions usually happen on the side of the body opposite the birthmark which vary in severity. There may also be muscle weakness on the side of the body opposite the birthmark.

Some children will have developmental delays and cognitive delays; about 50% will have glaucoma (optic neuropathy often associated with increased intraocular pressure), which can be present at birth or develop later. Glaucoma can be expressed as leukocoria, which should include also further evaluation for retinoblastoma. Increased pressure within the eye can cause the eyeball to enlarge and bulge out of its socket (buphthalmos).

Sturge–Weber syndrome rarely affects other body organs.

In the beginning, medical officials defined ABCD syndrome by the four key characteristics of the syndrome. In the first case study of the Kurdish girl, researches described her as having "albinism and a black lock at the right temporo-occipital region along Blaschko lines, her eyelashes and brows were white, the irises in her eyes appeared to be blue, she had spots of retinal depigmentation, and she did not react to noise." The albinism is interesting in this diagnosis because the skin of an affected individual is albino pale besides the brown patches of mispigmented skin. The "black locks" described and seen in clinical pictures of the infants are thick patches of black hair above the ears that form a half circle reaching to the other ear to make a crest shape.

As identified in this first case study and stated in a dictionary of dermatologic syndromes, ABCD syndrome has many notable features, including "snow white hair in patches, distinct black locks of hair, skin white except brown macules, deafness, irises gray to blue, nystagmus, photophobia, poor visual activity, normal melanocytes in pigmented hair and skin, and absent melanocytes in areas of leukoderma." Individuals have the blue/gray irises typical of people affected by blindness. The C of ABCD syndrome is what distinguishes this genetic disorder from BADS and it involves cell migration disorder of the neurocytes of the gut. This characteristic occurs when nerve cells do not function correctly in the gut, which results in aganglionosis: The intestines’ failure to move food along the digestive tract. Deafness or being unresponsive to noise due to very low quality of hearing was reported in every case of ABCD syndrome. The characteristics of ABCD syndrome are clearly evident in an inflicted individual.

No longer considered a separate syndrome, ABCD syndrome is today considered to be a variation of Shah-Waardenburg type IV. Waardenburg syndrome (WS) is described as "the combination of sensorineural hearing loss, hypopigmentation of skin and hair, and pigmentary disturbances of the irides." Hearing loss and deafness, skin mispigmentation and albinism, and pigmentary changes in irises are the similarities between WS and ABCD. According to a dictionary of dermatologic syndromes, Waardenburg syndrome has many notable features, including "depigmentation of hair and skin – white forelock and premature graying of hair, confluent thick eyebrows, heterochromic irides or hypopigmentation of iris, laterally displaced inner canthi, congenital sensorineural deafness, broad nasal root, autosomal dominant disorder, and other associated findings, including black forelocks."

Dysplastic nails are a cutaneous condition, and may be a subtle finding of ridging, flaking, or poor growth of the nails, or more diffuse with nearly complete loss of nails. This condition may be seen in a number of syndromes, including Dyskeratosis congenita and Nail–patella syndrome.