Individuals with KSS present initially in a similar way to those with typical CPEO. Onset is in the first and second decades of life.

The first symptom of this disease is a unilateral ptosis, or difficulty opening the eyelids, that gradually progresses to a bilateral ptosis. As the ptosis worsens, the individual commonly extends their neck, elevating their chin in an attempt to prevent the eyelids from occluding the visual axis. Along with the insidious development of ptosis, eye movements eventually become limited causing a person to rely more on turning the head side to side or up and down to view objects in the peripheral visual field.

KSS results in a pigmentation of the retina, primarily in the posterior fundus. The appearance is described as a "salt-and-pepper" appearance. There is diffuse depigmentation of the retinal pigment epithelium with the greatest effect occurring at the macula. This is in contrast to retinitis pigmentosa where the pigmentation is peripheral. The appearance of the retina in KSS is similar to that seen in myotonic dystrophy type 1 (abbreviated DM1). Modest night-blindness can be seen in patients with KSS. Visual acuity loss is usually mild and only occurs in 40–50% of patients.

CPEO is a slowly progressing disease. It may begin at any age and progresses over a period of 5–15 years. The first presenting symptom of ptosis is often unnoticed by the patient until the lids droop to the point of producing a visual field defect. Often, patients will tilt the head backwards to adjust for the slowly progressing ptosis of the lids. In addition, as the ptosis becomes complete, the patients will use the frontalis (forehead) muscle to help elevate the lids. The ptosis is typically bilateral, but may be unilateral for a period of months to years before the fellow lid becomes involved.

Ophthalmoplegia or the inability or difficulty to move the eye is usually symmetrical. As such, double vision is sometimes a complaint of these patients. The progressive ophthalmoplegia is often unnoticed till decreased ocular motility limits peripheral vision. Often someone else will point out the ocular disturbance to the patient. Patients will move their heads to adjust for the loss of peripheral vision caused by inability to abduct or adduct the eye. All directions of gaze are affected; however, downward gaze appears to be best spared. This is in contrast to progressive supranuclear palsy (PSP), which typically affects vertical gaze and spares horizontal gaze.

CPEO is a rare disease that may affect those of all ages, but typically manifests in the young adult years. CPEO is the most common manifestation of mitochondrial myopathy, occurring in an estimated two-thirds of all cases of mitochondrial myopathy. Patients typically present with ptosis (drooping eyelids). Other diseases like Graves' disease, myasthenia gravis and glioma that may cause an external ophthalmoplegia must be ruled out.

The generalized, common presentation for this broad and inclusive group of diseases is painless, bilateral loss of visual acuity and pallor of the optic disc accompanied with varying degrees of dyschromatopsia and central/cecocentral scatomas. On examination the papillary response may be sluggish to light, one would not expect to find an afferent papillary defect. This is because optic neuropathies are often bilateral and symmetric. The optic disc may be mildly hyperemic with small splinter hemorrhages on or around the disc. Optic atrophy may early on be non-existent and only later become mild. In later stages the optic atrophy is severe and this indicates less opportunity for recovery.

The duration of onset can vary between immediate and insidious, owing to the specific etiology. Two key features may be helpful in distinguishing acquired from inherited optic neuropathies: absence of a family history and simultaneous involvement of both eyes; the former more commonly characterized by these two features.

This is a rare autosomal recessive disorder characterized by early-onset optic atrophy, ataxia, and spasticity.

In the recessive form corneal clouding is observed at birth or within the neonatal period, nystagmus is often present, but no photophobia or epiphora is seen. In the autosomal dominant type corneal opacification is usually seen in the first or second year of life and progresses slowly, and nystagmus is infrequently seen.

Congenital hereditary corneal dystrophy (CHED) is a form of corneal dystrophy which presents at birth.

Megalocornea (MGCN, MGCN1) is an extremely rare nonprogressive condition in which the cornea has an enlarged diameter, reaching and exceeding 13 mm. It is noted in some patients with Marfan syndrome. It is thought to have two subforms, one with autosomal inheritance and the other X-linked (Xq21.3-q22). The X-linked form is more common and males generally constitute 90% of cases.

The most common presentation of Milroy Disease is bilateral lower extremity lymphedema, and may also be accompanied by hydrocele.

Cornea plana 1 (CNA1) is an extremely rare congenital hereditary deformity of the eye surface, leading to severe decrease in corneal curvature.

Signs and symptoms include (for each of the following causes):

- Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like syndrome (MELAS)

- Varying degrees of cognitive impairment and dementia

- Lactic acidosis

- Strokes

- Transient ischemic attacks

- Hearing loss

- Weight loss

- Myoclonic epilepsy and ragged-red fibers (MERRF)

- Progressive myoclonic epilepsy

- Clumps of diseased mitochondria accumulate in muscle fibers and appear as "ragged-red fibers" when muscle is stained with modified Gömöri trichrome stain

- Short stature

- Kearns-Sayre syndrome (KSS)

- External ophthalmoplegia

- Cardiac conduction defects

- Sensorineural hearing loss

- Chronic progressive external ophthalmoplegia (CPEO)

- Progressive ophthalmoparesis

- Symptomatic overlap with other mitochondrial myopathies

Diagnostic methods vary, and are based on specific possible etiologies; however, an X-ray computed tomography scan of the face (or magnetic resonance imaging, or both) may be helpful.

Cornea plana 2 (CNA2) is an extremely rare congenital hereditary deformity of the eye surface, leading to severe decrease in corneal curvature. There is evidence that cornea plana 2 is caused by mutations in KERA gene encoding "keratocan".

The most common finding is oculomotor nerve dysfunction leading to ophthalmoplegia. This is often accompanied by ophthalmic nerve dysfunction, leading to hypoesthesia of the upper face. The optic nerve may eventually be involved, with resulting visual impairment.

Oguchi disease present with nonprogressive night blindness since young childhood or birth with normal day vision, but they frequently claim improvement of light sensitivities when they remain for some time in a darkened environment.

On examination patients have normal visual fields but the fundos have a diffuse or patchy, silver-gray or golden-yellow metallic sheen and the retinal vessels stand out in relief against the background.

A prolonged dark adaptation of three hours or more, leads to disappearance of this unusual discoloration and the appearance of a normal reddish appearance. This is known as the Mizuo-Nakamura phenomena and is thought to be caused by the overstimulation of rod cells.

Like other mitochrondrial diseases, "MNGIE is a multisystem disorder". MNGIE primarily affects the gastrointestinal and neurological systems. Gastrointestinal symptoms may include gastrointestinal dysmotility, due to inefficient peristalsis, which may result in pseudo-obstruction and cause malabsorption of nutrients. Additionally, gastrointestinal symptoms such as borborygmi, early satiety, diarrhea, constipation, gastroparesis, nausea, vomiting, weight loss, and diverticulitis may be present in MNGIE patients. Neurological symptoms may include diffuse leukoencephalopathy, peripheral neuropathy, and myopathy. Ocular symptoms may include retinal degeneration, ophthalmoplegia, and ptosis. Those with MNGIE are often thin and experience continuous weight loss. The characteristic thinness of MNGIE patients is caused by multiple factors including inadequate caloric intake due to gastrointestinal symptoms and discomfort, malabsorption of food from bacterial overgrowth due to decreased motility, as well as an increased metabolic demand due to inefficient production of ATP by the mitochondria.

VLDLR-associated cerebellar hypoplasia (VLDLRCH; alternative names: dysequilibrium syndrome, DES; nonprogressive cerebellar disorder with mental retardation) is a rare autosomal recessive condition caused by a disruption of the VLDLR gene. First described as a form of cerebral palsy in the 1970s, it is associated with parental consanguinity and is found in secluded communities, with a number of cases described in Hutterite families.

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).

Milroy's disease (MD) is a familial disease characterized by lymphedema, commonly in the legs, caused by congenital abnormalities in the lymphatic system. Disruption of the normal drainage of lymph leads to fluid accumulation and hypertrophy of soft tissues. It is also known as Milroy disease, Nonne-Milroy-Meige syndrome and hereditary lymphedema.

It was named by Sir William Osler for William Milroy, a Canadian physician, who described a case in 1892, though it was first described by Rudolf Virchow in 1863.

The clinical presentation of HFM is quite variable. The severity may depend on the extent of the area with an insufficient blood supply "in utero", and the gestational age of the fetus at which this occurs. In some people, the only physical manifestation may be a small and underdeveloped external ear. In more severe cases, multiple parts of the face may be affected. Some people with HFM may have sensorineural hearing loss and decreased visual acuity or even blindness.

Goldenhar syndrome can be thought of as a particularly severe form of HFM, in which extracranial anomalies are present to some extent. Some of the internal organs (especially the heart, kidneys, and lungs) may be underdeveloped, or in some cases even absent altogether. The affected organs are typically on the same side as the affected facial features, but bilateral involvement occurs in approximately 10% of cases. Deformities of the vertebral column such as scoliosis may also be observed in Goldenhar syndrome.

While there is no universally accepted grading scale, the OMENS scale (standing for Orbital, Mandible, Ear, Nerves and Soft tissue) was developed to help describe the heterogeneous phenotype that makes up this sequence or syndrome.

Intellectual disability is not typically seen in people with HFM.

Other conditions with similar appearing fundi include

- Cone dystrophy

- X-linked retinitis pigmentosa

- Juvenile macular dystrophy

These conditions do not show the Mizuo-Nakamura phenomenon.

Ophthalmoparesis can involve any or all of the extraocular muscles, which include the superior recti, inferior recti, medial recti, lateral recti, inferior oblique and superior oblique muscles.

It can also be classified by the directions of affected movements, e.g. "vertical ophthalmoparesis".

Parinaud's Syndrome is a cluster of abnormalities of eye movement and pupil dysfunction, characterized by:

1. Paralysis of upgaze: Downward gaze is usually preserved. This vertical palsy is supranuclear, so doll's head maneuver should elevate the eyes, but eventually all upward gaze mechanisms fail.

2. Pseudo-Argyll Robertson pupils: Accommodative paresis ensues, and pupils become mid-dilated and show light-near dissociation.

3. Convergence-Retraction nystagmus: Attempts at upward gaze often produce this phenomenon. On fast up-gaze, the eyes pull in and the globes retract. The easiest way to bring out this reaction is to ask the patient to follow down-going stripes on an optokinetic drum.

4. Eyelid retraction (Collier's sign)

5. Conjugate down gaze in the primary position: "setting-sun sign". Neurosurgeons see this sign most commonly in patients with failed hydrocephalus shunts.

It is also commonly associated with bilateral papilledema. It has less commonly been associated with spasm of accommodation on attempted upward gaze, pseudoabducens palsy (also known as thalamic esotropia) or slower movements of the abducting eye than the adducting eye during horizontal saccades, see-saw nystagmus and associated ocular motility deficits including skew deviation, oculomotor nerve palsy, trochlear nerve palsy and internuclear ophthalmoplegia.

Causes of the one and a half syndrome include pontine hemorrhage, ischemia, tumors, infective mass lesions such as tuberculomas, and demyelinating conditions like multiple sclerosis.