There is currently no defined treatment to ameliorate the muscle weakness of CPEO. Treatments used to treat other pathologies causing ophthalmoplegia has not been shown to be effective.

Experimental treatment with tetracycline has been used to improve ocular motility in one patient. Coenzyme Q has also been used to treat this condition. However, most neuro-ophthalmologists do not ascribe to any treatment.

Ptosis associated with CPEO may be corrected with surgery to raise the lids, however due to weakness of the orbicularis oculi muscles, care must be taken not to raise the lids in excess causing an inability to close the lids. This results in an exposure keratopathy. Therefore, rarely should lid surgery be performed and only by a neuro-ophthalmologist familiar with the disease.

The most common strabismus finding is large angle exotropia which can be treated by maximal bilateral eye surgery, but due to the progressive nature of the disease, strabismus may recur. Those that have diplopia as a result of asymmetric ophthalmoplegia may be corrected with prisms or with surgery to create a better alignment of the eyes.

Currently there is no curative treatment for KSS. Because it is a rare condition, there are only case reports of treatments with very little data to support their effectiveness. Several promising discoveries have been reported which may support the discovery of new treatments with further research. Satellite cells are responsible for muscle fiber regeneration. It has been noted that mutant mtDNA is rare or undetectable in satellite cells cultured from patients with KSS. Shoubridge et al. (1997) asked the question whether wildtype mtDNA could be restored to muscle tissue by encouraging muscle regeneration. In the forementioned study, regenerating muscle fibers were sampled at the original biopsy site, and it was found that they were essentially homoplasmic for wildtype mtDNA. Perhaps with future techniques of promoting muscle cell regeneration and satellite cell proliferation, functional status in KSS patients could be greatly improved.

One study described a patient with KSS who had reduced serum levels of coenzyme Q10. Administration of 60–120 mg of Coenzyme Q10 for 3 months resulted in normalization of lactate and pyruvate levels, improvement of previously diagnosed first degree AV block, and improvement of ocular movements.

A screening ECG is recommended in all patients presenting with CPEO. In KSS, implantation of pacemaker is advised following the development of significant conduction disease, even in asymptomatic patients.

Screening for endocrinologic disorders should be performed, including measuring serum glucose levels, thyroid function tests, calcium and magnesium levels, and serum electrolyte levels. Hyperaldosteronism is seen in 3% of KSS patients.

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

Treatment of THS includes immunosuppressives such as corticosteroids (often prednisolone) or steroid-sparing agents (such as methotrexate or azathioprine).

Radiotherapy has also been proposed.

Conservative treatment involves the long term use of laxatives and enemas, and has limited success. Dietary changes in order to control the disease are ineffective and high fiber diets often worsen the symptoms in children. As a last resort, surgical treatment (internal sphincter myectomy or colon resection) is used. In extreme cases, the only effective cure is a complete transplant of the affected parts.

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

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.

Children with blue diaper syndrome are put on restricted diets. This is in effort to reduce kidney damage. Restrictions include: calcium, protein, vitamin D, and tryptophan. Calcium is restricted to help prevent kidney damage. Examples of food with high levels of tryptophan include turkey and warm milk.

Antibiotics may be used to control or eliminate particular intestinal bacteria. Nicotinic acid may be used to control intestinal infections.

Genetic counseling can also be beneficial, as well as taking part in clinical trials.

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.

Aponeurotic and congenital ptosis may require surgical correction if severe enough to interfere with vision or if cosmetics is a concern.

Treatment depends on the type of ptosis and is usually performed by an ophthalmic plastic and reconstructive surgeon, specializing in diseases and problems of the eyelid.

Surgical procedures include:

- Levator resection

- Müller muscle resection

- Frontalis sling operation (preferred option for oculopharyngeal muscular dystrophy)

Non-surgical modalities like the use of "crutch" glasses or Ptosis crutches or special scleral contact lenses to support the eyelid may also be used.

Ptosis that is caused by a disease may improve if the disease is treated successfully, although some related diseases, such as oculopharyngeal muscular dystrophy currently have no treatments or cures.

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.

Most patients reported in the literature have been given treatments suitable for autoimmune neurological diseases, such as corticosteroids, plasmapheresis and/or intravenous immunoglobulin, and most have made a good recovery. The condition is too rare for controlled trials to have been undertaken.

Differentiation of DIOS from constipation is generally performed by unit specializing in the treatment of cystic fibrosis. Adequate hydration and an aggressive regimen of laxatives are essential for treatment and prevention of DIOS. Osmotic laxatives such as polyethylene glycol are preferred. Individuals prone to DIOS tend to be at risk for repeated episodes and often require maintenance therapy with pancreatic enzyme replacement, hydration and laxatives (if the symptoms are also mild).

Oral contrast instillation into the colon/ileum under radiological control has been found to reduce the need for surgical intervention.

Prevention focuses on improving sanitation of water and food sources.

Treatment focuses on addressing the central components of intestinal inflammation, bacterial overgrowth and nutritional supplementation.

SMA syndrome can present in acute, acquired form (e.g. abruptly emerging within an inpatient stay following scoliosis surgery) as well as chronic form (i.e. developing throughout the course of a lifetime and advancing due to environmental triggers, life changes, or other illnesses). According to a number of recent sources, at least 70% of cases can typically be treated with medical treatment, while the rest require surgical treatment.

Medical treatment is attempted first in many cases. In some cases, emergency surgery is necessary upon presentation. A six-week trial of medical treatment is recommended in pediatric cases. The goal of medical treatment for SMA Syndrome is resolution of underlying conditions and weight gain. Medical treatment may involve nasogastric tube placement for duodenal and gastric decompression, mobilization into the prone or left lateral decubitus position, the reversal or removal of the precipitating factor with proper nutrition and replacement of fluid and electrolytes, either by surgically inserted jejunal feeding tube, nasogastric intubation, or peripherally inserted central catheter (PICC line) administering total parenteral nutrition (TPN). Pro-motility agents such as metoclopramide may also be beneficial. Symptoms may improve after restoration of weight, except when reversed peristalsis persists, or if regained fat refuses to accumulate within the mesenteric angle. Most patients seem to benefit from nutritional support with hyperalimentation irrespective of disease history.

If medical treatment fails, or is not feasible due to severe illness, surgical intervention is required. The most common operation for SMA syndrome, duodenojejunostomy, was first proposed in 1907 by Bloodgood. Performed as either an open surgery or laparoscopically, duodenojejunostomy involves the creation of an anastomosis between the duodenum and the jejunum, bypassing the compression caused by the AA and the SMA. Less common surgical treatments for SMA syndrome include Roux-en-Y duodenojejunostomy, gastrojejunostomy, anterior transposition of the third portion of the duodenum, intestinal derotation, division of the ligament of Treitz (Strong's operation), and transposition of the SMA. Both transposition of the SMA and lysis of the duodenal suspensory muscle have the advantage that they do not involve the creation of an intestinal anastomosis.

The possible persistence of symptoms after surgical bypass can be traced to the remaining prominence of reversed peristalsis in contrast to direct peristalsis, although the precipitating factor (the duodenal compression) has been bypassed or relieved. Reversed peristalsis has been shown to respond to duodenal circular drainage—a complex and invasive open surgical procedure originally implemented and performed in China.

In some cases, SMA Syndrome may occur alongside a serious, life-threatening condition such as cancer or AIDS. Even in these cases, though, treatment of the SMA Syndrome can lead to a reduction in symptoms and an increased quality of life.

A health care provider may prescribe octreotide acetate (Sandostatin) injections to treat dumping syndrome symptoms. The medication works by slowing gastric emptying and inhibiting the release of insulin and other GI hormones.

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

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.

The first step to minimizing symptoms of dumping syndrome involves changes in eating, diet, and nutrition, and may include

- eating five or six small meals a day instead of three larger meals

- delaying liquid intake until at least 30 minutes after a meal

- increasing intake of protein, fiber, and complex carbohydrates—found in starchy foods such as oatmeal and rice

- avoiding simple sugars such as table sugar, which can be found in candy, syrup, sodas, and juice beverages

- increasing the thickness of food by adding pectin or guar gum—plant extracts used as thickening agents

Some people find that lying down for 30 minutes after meals also helps reduce symptoms, though some health care providers advise against this.

While the disease manifests early in life in most cases, diagnosis of the disease is often quite delayed. The symptoms that affected patients present vary, but the most common presenting symptoms are gastrointestinal issues such as nausea, vomiting, abdominal pain, and diarrhea, and neurologic or ocular symptoms such as hearing loss, weakness, and peripheral neuropathy. These gastrointestinal symptoms cause patients with MNGIE to be very thin and experience persistent weight loss and this often leads to MNGIE being misdiagnosed as an eating disorder. These symptoms without presentation of disordered eating and warped body image warrant further investigation into the possibility of MNGIE as a diagnosis. Presentation of these symptoms and lack of disordered eating are not enough for a diagnosis. Radiologic studies showing hypoperistalsis, large atonic stomach, dilated duodenum, diverticula, and white matter changes are required to confirm the diagnosis. Elevated blood and urine nucleoside levels are also indicative of MNGIE syndrome. Abnormal nerve conduction as well as analysis of mitochondria from liver, intestines, muscle, and nerve tissue can also be used to support the diagnosis.

A successful treatment for MNGIE has yet to be found, however, symptomatic relief can be achieved using pharmacotherapy and celiac plexus neurolysis. Celiac plexus neurolysis involves interrupting neural transmission from various parts of the gastrointestinal tract. By blocking neural transmission, pain is relieved and gastrointestinal motility increases. Stem cell therapies are currently being investigated as a potential cure for certain patients with the disease, however, their success depends on physicians catching the disease early before too much organ damage has occurred.

Possible treatments include:

- In stable cases, use of laxatives and bulking agents, as well as modifications in diet and stool habits are effective.

- Corticosteroids and other anti-inflammatory medication is used in toxic megacolon.

- Antibiotics are used for bacterial infections such as oral vancomycin for "Clostridium difficile"

- Disimpaction of feces and decompression using anorectal and nasogastric tubes.

- When megacolon worsens and the conservative measures fail to restore transit, surgery may be necessary.

- Bethanechol can also be used to treat megacolon by means of its direct cholinergic action and its stimulation of muscarinic receptors which bring about a parasympathetic like effect.

There are several surgical approaches to treat megacolon, such as a colectomy (removal of the entire colon) with ileorectal anastomosis (ligation of the remaining ileum and rectum segments), or a total proctocolectomy (removal of colon, sigmoid and rectum) followed by ileostomy or followed by ileoanal anastomosis.

There are multiple large-field, multi-country research initiatives focusing on strategies to prevent and treat EE.

- The MAL-ED project

- The Alive and Thrive nutrition project

- The Sanitation, Hygiene and Infant Nutrition Efficacy (SHINE) Trial (ClinicalTrials.gov identifier: NCT01824940)

- The WASH Benefits Study

The main symptom of enteric neuropathy is severe and constant pain. Other symptoms include nausea, vomiting, diarrhoea, constipation, bloating and abdominal abnormalities. In addition malabsorption and poor nutrition are common, as the digestive system begins to fail. Symptom management is very important and the main priority is usually to get on top of the pain. However, as most people may have been waiting for years for a diagnosis they are often already addicted to painkillers (such as tramadol and oramorph) and these have adverse effects on the primary condition.

Secondary chronic intestinal pseudo-obstruction is managed by treating the underlying condition.

There is no cure for primary chronic intestinal pseudo-obstruction. It is important that nutrition and hydration is maintained, and pain relief is given. Drugs that increase the propulsive force of the intestines have been tried, as have different types of surgery.