Kearns–Sayre syndrome occurs spontaneously in the majority of cases. In some cases it has been shown to be inherited through mitochondrial, autosomal dominant, or autosomal recessive inheritance. There is no predilection for race or sex, and there are no known risk factors. As of 1992 there were only 226 cases reported in published literature.

Chronic progressive external ophthalmoplegia (CPEO), also known as progressive external ophthalmoplegia (PEO), is a type of eye disorder characterized by slowly progressive inability to move the eyes and eyebrows. It is often the only feature of mitochondrial disease, in which case the term CPEO may be given as the diagnosis. In other people suffering from mitochondrial disease, CPEO occurs as part of a syndrome involving more than one part of the body, such as Kearns-Sayre syndrome. Occasionally CPEO may be caused by conditions other than mitochondrial diseases.

Kearns–Sayre syndrome (KSS) is a mitochondrial myopathy with a typical onset before 20 years of age. KSS is a more severe syndromic variant of chronic progressive external ophthalmoplegia (abbreviated CPEO), a syndrome that is characterized by isolated involvement of the muscles controlling movement of the eyelid (levator palpebrae, orbicularis oculi) and eye (extra-ocular muscles). This results in ptosis and ophthalmoplegia respectively. KSS involves a combination of the already described CPEO as well as pigmentary retinopathy in both eyes and cardiac conduction abnormalities. Other symptoms may include cerebellar ataxia, proximal muscle weakness, deafness, diabetes mellitus, growth hormone deficiency, hypoparathyroidism, and other endocrinopathies. In both of these diseases, muscle involvement may begin unilaterally but always develops into a bilateral deficit, and the course is progressive. This discussion is limited specifically to the more severe and systemically involved variant.

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.

Congenital fibrosis of the extraocular muscles, or CFEOM, is a class of rare genetic disorders affecting one or more of the muscles that move the eyeballs. Individuals with CFEOM have varying degrees of ophthalmoplegia (an inability to move the eyes in one or more directions) and ptosis. The condition is present from birth and non-progressive, runs in families, and usually affects both eyes similarly. In the most common form, the superior recti are dysfunctional and the inferior recti, lacking proper opposition, pull the eyes down, forcing the head to be tilted upward in order to see straight ahead.

There are three types of CFEOM, numbered 1-3. CFEOM1, the most common type, is now known to be caused by one of several mutations in the KIF21A gene, while CFEOM2 is caused by mutations in the PHOX2A gene. CFEOM3 is caused by mutations in the TUBB3 gene.

CFEOM was first named in 1956, although papers describing conditions now known or assumed to be CFEOM appear in the medical literature as early as 1840. Due to its rarity, it has been independently cited numerous times under many different names.

Microvillus inclusion disease is thought to be extremely rare; only approximately 200 cases have been identified in children in Europe.

One patient, a teenage female living in Arizona, suddenly began to grow microvilli after thirteen years of TPN (Total Parenteral Nutrition) and Lipid dependency. She now enjoys a typical teenage diet and is seen regularly by her Gastroenterologist.

One patient from the UK was documented to achieve nutritional independence at age 3.

On 26 June 2009 a six-year-old girl diagnosed with microvillus inclusion disease became the third person in the UK to die of swine flu.

Although no cure currently exists, there is hope in treatment for this class of hereditary diseases with the use of an embryonic mitochondrial transplant.

There have been cases of improvement in extra-ocular movement with botulinum toxin injection.

The diagnosis of enteric neuropathy is rather difficult, in that many symptoms present in ways that are common to many other bowel- and gut-related diseases. It is common that many people undergo many surgeries, sometimes over several years, to attempt to combat other possible diseases. The diagnosis itself is conducted by a physician based on multiple tests and is subjective rather than definitive, which for those who have enteric neuropathy will show signs of severe abnormalities in the movement of the gut. An operation to take a section of muscle for biopsy which, if it shows signs of nerve degradation, assists in the diagnosis.

The prognosis of THS is usually considered good. Patients usually respond to corticosteroids, and spontaneous remission can occur, although movement of ocular muscles may remain damaged. Roughly 30–40% of patients who are treated for THS experience a relapse.

Mitochondrial neurogastrointestinal encephalopathy syndrome (MNGIE) is a rare autosomal recessive mitochondrial disease. It has been previously referred to as polyneuropathy, ophthalmoplegia, leukoencephalopathy, and POLIP syndrome. The disease presents in childhood, but often goes unnoticed for decades. Unlike typical mitochondrial diseases caused by mitochondrial DNA (mtDNA) mutations, MNGIE is caused by mutations in the TYMP gene, which encodes the enzyme thymidine phosphorylase. Mutations in this gene result in impaired mitochondrial function, leading to intestinal symptoms as well as neuro-ophthalmologic abnormalities. "A secondary form of MNGIE, called MNGIE without leukoencephalopathy, can be caused by mutations in the POLG gene".

Ophthalmoparesis can result from disorders of various parts of the eye and nervous system:

- Infection around the eye. Ophthalmoplegia is an important finding in orbital cellulitis.

- The orbit of the eye, including mechanical restrictions of eye movement, as in Graves disease.

- The muscle, as in progressive external ophthalmoplegia or Kearns-Sayre syndrome.

- The neuromuscular junction, as in myasthenia gravis.

- The relevant cranial nerves (specifically the oculomotor, trochlear, and abducens), as in cavernous sinus syndrome or raised intracranial pressure.

- The brainstem nuclei of these nerves, as in certain patterns of brainstem stroke such as Foville's syndrome.

- White matter tracts connecting these nuclei, as in internuclear ophthalmoplegia, an occasional finding in multiple sclerosis.

- Dorsal midbrain structures, as in Parinaud's syndrome.

- Certain parts of the cerebral cortex (including the frontal eye fields), as in stroke.

- Toxic envenomation by mambas, taipans, and kraits.

Thiamine deficiency can cause ophthalmoparesis in susceptible persons; this is part of the syndrome called Wernicke encephalopathy. The causal pathway by which this occurs is unknown. Intoxication with certain substances, such as phenytoin, can also cause ophthalmoparesis.

It is nearly always fatal unless, like short bowel syndrome patients, treated with parenteral nutrition or an intestinal transplant. The patient is often classified as being in "intestinal failure" and treated with the cohort of patients known as "short bowel syndrome" patients.

Enteric neuropathy is a degenerative neuromuscular condition of the digestive system. In simple terms the gut stops functioning, due to degradation of the nerves and muscles. The condition affects all parts of the digestive tract. There is no known cure or treatment for enteric neuropathy at this time; it is only possible to work on symptom management.

The name enteric neuropathy only seems to be used for diagnosis within the UK. The most common name worldwide for this condition is Intestinal pseudoobstruction.

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.

Treatment and prognosis depend on the underlying condition. For example, in thiamine deficiency, treatment would be the immediate administration of vitamin B1.

THS is uncommon in both the United States and internationally. In New Zealand, there is only one recorded case, there is also one recorded case in New South Wales, Australia. Both genders, male and female, are affected equally, and it typically occurs around the age of 60.

Parinaud's Syndrome results from injury, either direct or compressive, to the dorsal midbrain. Specifically, compression or ischemic damage of the mesencephalic tectum, including the superior colliculus adjacent oculomotor (origin of cranial nerve III) and Edinger-Westphal nuclei, causing dysfunction to the motor function of the eye.

Classically, it has been associated with three major groups:

1. Young patients with brain tumors in the pineal gland or midbrain: pinealoma (intracranial germinomas) are the most common lesion producing this syndrome.

2. Women in their 20s-30s with multiple sclerosis

3. Older patients following stroke of the upper brainstem

However, any other compression, ischemia or damage to this region can produce these phenomena: obstructive hydrocephalus, midbrain hemorrhage, cerebral arteriovenous malformation, trauma and brainstem toxoplasmosis infection. Neoplasms and giant aneurysms of the posterior fossa have also been associated with the midbrain syndrome.

Vertical supranuclear ophthalmoplegia has also been associated with metabolic disorders, such as Niemann-Pick disease, Wilson's disease, kernicterus, and barbiturate overdose.

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.

Mitochondrial myopathies are types of myopathies associated with mitochondrial disease. On biopsy, the muscle tissue of patients with these diseases usually demonstrate "ragged red" muscle fibers. These ragged-red fibers contain mild accumulations of glycogen and neutral lipids, and may show an increased reactivity for succinate dehydrogenase and a decreased reactivity for cytochrome c oxidase. Inheritance was believed to be maternal (non-Mendelian extranuclear). It is now known that certain nuclear DNA deletions can also cause mitochondrial myopathy such as the OPA1 gene deletion. There are several subcategories of mitochondrial myopathies.

Berdon syndrome, also called Megacystis-microcolon-intestinal hypoperistalsis syndrome (MMIH syndrome), is an autosomal recessive fatal genetic disorder affecting newborns. In a 2011 study of 227 children with the syndrome, "the oldest survivor [was] 24 years old." The Ann Arbor News reported a five year old survivor at the end of 2015.

It is more prevalent in females, 7 females to 3 males, and is characterized by constipation and urinary retention, microcolon, giant bladder (megacystis), intestinal hypoperistalis, hydronephrosis, and dilated small bowel. The pathological findings consist of an abundance of ganglion cells in both dilated and narrow areas of the intestine. It is a familial disturbance of unknown cause.

Walter Berdon "et al." in 1976 first described the condition in five female infants, two of whom were sisters. All had marked dilatation of the bladder and some had hydronephrosis and the external appearance of prune belly. The infants also had microcolon and dilated small intestines.

The eye findings of Parinaud's Syndrome generally improve slowly over months, especially with resolution of the causative factor; continued resolution after the first 3–6 months of onset is uncommon. However, rapid resolution after normalization of intracranial pressure following placement of a ventriculoperitoneal shunt has been reported.

Treatment is primarily directed towards etiology of the dorsal midbrain syndrome. A thorough workup, including neuroimaging is essential to rule out anatomic lesions or other causes of this syndrome. Visually significant upgaze palsy can be relieved with bilateral inferior rectus recessions. Retraction nystagmus and convergence movement are usually improved with this procedure as well.

A variety of mutations in the TYMP gene have been discovered that lead to the onset of mitochondrial neurogastrointestinal encephalopathy syndrome. The TYMP gene is a nuclear gene, however, mutations in the TYMP gene affect mitochrondrial DNA and function. Mutations in this gene result in a loss of thymidine phosphorylase activity. Thymidine phosphorylase is the enzymatic product of the TYMP gene and is responsible for breaking down thymidine nucleosides into thymine and 2-deoxyribose 1-phosphate. Without normal thymidine phosphorylase activity, thymidine nucleosides begin to build up in cells. High nucleoside levels are toxic to mitochondrial DNA and cause mutations that lead to dysfunction of the respiratory chain, and thus, inadequate energy production in the cells. These mitochondrial effects are responsible for the symptomatology associated with the disease.

Orbital apex syndrome, also known as Jacod syndrome, is a collection of cranial nerve deficits associated with a mass lesion near the apex of the orbit of the eye. This syndrome is a separate entity from Rochon–Duvigneaud syndrome, which occurs due to a lesion immediately anterior to the orbital apex. Most commonly optic nerve is involved.

Hennekam syndrome also known as intestinal lymphagiectasia–lymphedema–mental retardation syndrome, is an autosomal recessive disorder consisting of intestinal lymphangiectasia, facial anomalies, peripheral lymphedema, and mild to moderate levels of growth and intellectual disability.

It is also known as "lymphedema-lymphangiectasia-mental retardation syndrome".

In a subset of patients it is associated with CCBE1 according research published by its namesake, Raoul Hennekam. Other causal mutations were found in the FAT4 gene. Previously, mutations in the FAT4 gene had been only associated with van Maldergem syndrome. The molecular mechanism of the lymphedema phenotype in CCBE1-associated cases was identified as a diminished ability of the mutated CCBE1 to accelerate and focus the activation of the primary lymphangiogenic growth factor VEGF-C.