There no standardized effective treatment strategies for the condition. Severe fatal respiratory failure can develop; long-term treatment with macrolides such as clarithromycin, erythromycin and azithromycin has been empirically applied for the treatment of primary ciliary dyskinesia in Japan, though controversial due to the effects of the medications.

Orofaciodigital syndrome type 1 can be treated with reconstructive surgery or the affected parts of the body. Surgery of cleft palate, tongue nodules, additional teeth, accessory frenulae, and orthodontia for malocclusion. Routine treatment for patients with renal disease and seizures may also be necessary. Speech therapy and special education in the later development may also be used as management.

There is no causative / curative therapy. Symptomatic medical treatments are focussing on symptoms caused by orthopaedic, dental or cardiac problems. Regarding perioperative / anesthesiological management, recommendations for medical professionals are published at OrphanAnesthesia.

There is no cure for Alström syndrome; however, there are treatment aims to reduce the symptoms and prevent further complications. Some of these treatment aims include:

- Corrective lenses: tinted lenses that help with the sensitivity from bright lights. The patients may have to adapt to reading in Braille, use adaptive equipment, mobility aids, and adaptive computing skills.

- Education: patients with Alström syndrome suffering from intellectual disabilities must have access to education. They must be able to receive free and appropriate education. Some Alström syndrome patients are educated in normal classrooms. Other patients have to take special education classes or attend to specialized schools that are prepared to teach children with disabilities. Staff members from schools have to consult with patient's parents or caregivers in order to design an education plan based on the child's needs. In addition, the school may document the progress of the child in order to confirm that the child's needs are being met.

- Hearing aids: the battery-operated devices are available in three styles: behind the ear, in the ear, and inside the ear canal. Behind the ear aims for mild-to-profound hearing loss. In the ear aims for mild to severe hearing loss. Lastly, the canal device is aimed for mild to moderately severe hearing loss. Patients that have severe hearing loss may benefit from a cochlear implant.

- Diet: an appropriate and healthy diet is necessary for individuals with Alström syndrome because it could potentially decreases chances of obesity or diabetes.

- Occupational therapy: the therapist helps the child learn skills to help him or her perform basic daily tasks like eating, getting dressed, and communicating with others.

- Physical Activity: exercising reduces chances of being obese and helping control blood sugar levels.

- Dialysis: helps restore filtering function. With hemodialysis, a patient's blood circulates into an external filter and clean. The filtered blood is then returned into the body. With peritoneal dialysis, fluid containing dextrose is introduced into the abdomen by a tube. The solution then absorbs the wastes into the body and is then removed.

- Transplantation: patients that endure a kidney failure may undergo a kidney transplantation.

- Surgery: if the patient endures severe scoliosis or kyphosis, surgery may be required.

The management of this condition can be done via-improvement of any electrolyte imbalance, as well as, hypertension and anemia treatment as the individuals condition warrants.

Treatment for Joubert syndrome is symptomatic and supportive. Infant stimulation and physical, occupational, speech and hearing therapy may benefit some patients. Infants with abnormal breathing patterns should be monitored.

The syndrome is associated with progressive worsening for kidneys, the liver and the eyes and thus require regular monitoring.

Emanuel Syndrome does not have a cure, but individual symptoms may be treated. Assessments of individual systems, such as the cardiovascular, gastrointestinal, orthopedic, and neurological may be necessary to determine the extent of impairment and options for treatment.

There has been no treatment discovered for Jacobsen Syndrome until now but the Symptoms can be treated. 56% of children with Jacobsen Syndrome have congenital heart problems to keep them in check a baseline evaluation can be made by a paediatric cardiologist by carrying out an electrocardiogram or echocardiogram. Any problems that are found can be treated then.

Almost all affected children are born with a bleeding disorder, monthly CBT may help ease the problem. Consecutively Platelet transfusion and ddAVP can be carried out. Medication that interferes with platelet count should be avoided and oral contraceptive therapy may be considered for women with heavy bleeding during menses.

Children affected with Jacobsen Syndrome have severe to Moderate intellectual disabilities and cognitive impairment. An evaluation by a neuropsychologist or a behaviour specialist like a Psychiatrist or Psychologist can be performed, including brain imaging like MRI or ERP. Then as deemed appropriate intervention programs can be carried through. Music therapy is very beneficial for language development. According to the age, befitting vision and hearing test can aid in fixing problems related cognition. For problems related to behaviour like ADHD, medication or therapy would be required but a combination of both is more effective. An ophthalmologist should be consulted to treat the eye defects. Play and interactive games encourage the child to speak. Habilitiation in children should begin at an early age. A habilitation team includes professionals with special expertise in how disability affects everyday life, health and development. The entire family is supported to help the affected children and their families adjust better.

Treatment is limited. Drugs can alleviate the symptoms, such as sleep difficulties and epilepsy. Physiotherapy helps affected children retain the ability to remain upright for as long as possible, and prevents some of the pain.

Recent attempts to treat INCL with cystagon have been unsuccessful.

A 1998 review noted that life expectancy is usually normal, but that there have occasionally been reported neonatal deaths due to PCD. A 2016 longitudinal study followed 151 adults with PCD for a median of 7 years. Within that span, 7 persons died with a median age of 65.

Treatment for individuals with Dandy–Walker Syndrome generally consists of treating the associated problems, if needed.

A special tube (shunt) to reduce intracranial pressure may be placed inside the skull to control swelling. Endoscopic third ventriculostomy is also an option.

Treatment may also consist of various therapies such as occupational therapy, physiotherapy, speech therapy or specialized education. Services of a teacher of students with blindness/visual impairment may be helpful if the eyes are affected.

In a sample of 19 children, a 1997 study found that 3 died before the age of 3, and 2 never learned to walk. The children had various levels of delayed development with developmental quotients from 60 to 85.

Prevention for Alström Syndrome is considered to be harder compared to other diseases/syndromes because it is an inherited condition. However, there are other options that are available for parents with a family history of Alström Syndrome. Genetic testing and counseling are available where individuals are able to meet with a genetic counselor to discuss risks of having the children with the disease. The genetic counselor may also help determine whether individuals carry the defective ALSM1 gene before the individuals conceive a child. Some of the tests the genetic counselors perform include chorionic villus sampling (CVS), Preimplantation genetic diagnosis (PGD), and amniocentesis. With PGD, the embryos are tested for the ALSM1 gene and only the embryos that are not affected may be chosen for implantation via in vitro fertilization.

Children with WAGR syndrome receive regular (3-4 yearly) kidney surveillance for Wilms' tumour until at least the age of 6–8 years and thereafter remain under some follow-up because of the risk of late onset nephropathy (40% of patients over the age of 12 years). Females with WAGR syndrome may have streak ovaries, which can increase the risk for gonadoblastoma. Malformations of the vagina and/or uterus may also be present.

Potocki–Shaffer syndrome can be detected through array comparative genomic hybridization (aCGH).

Some symptoms can be managed with drug therapy, surgery and rehabilitation, genetic counselling, and palliative care.

Diagnosis of cortisone reductase deficiency is done through analysis of cortisol to cortisone metabolite levels in blood samples. As of now, there is no treatment for cortisone reductase deficiency. Shots of cortisol are quickly metabolised into cortisone by the dysregulated 11β-HSD1 enzyme; however, symptoms can be treated. Treatment of hyperandroginism can be done through prescription of antiandrogens. They do so by inhibiting the release of gonadotropin and luteinizing hormone, both hormones in the pituitary, responsible for the production of testosterone.

The use of surgery to treat the condition is controversial. Options include liposuction and lipectomy.

The studies of highest quality involve tumescent or super tumescent anesthesia and vibrating liposuction, powered, cannula used with lymph sparing techniques. The treatment of lipedema with tumescent liposuction requires multiple procedures. In the United States Health Insurance do not generally pay for liposuction for lipedema, making it expensive. Liposuction under general anesthesia, without tumescent anesthesia, can be damaging and is not recommended for the treatment.

The most effective anti-epileptic medication for JME is valproic acid (Depakote). Women are often started on alternative medications due to valproic acid's high incidence of fetal malformations. Lamotrigine, levetiracetam, topiramate, and zonisamide are alternative anti-epileptic medications with less frequent incidence of pregnancy related complications, and they are often used first in females of childbearing age. Carbamazepine may aggravate primary generalized seizure disorders such as JME. Treatment is lifelong. Patients should be warned to avoid sleep deprivation.

In GRA, the hypersecretion of aldosterone and the accompanying hypertension are remedied when ACTH secretion is suppressed by administering glucocorticoids.

Dexamethasone, spironolactone and eplerenone have been used in treatment.

A 1994 review of 150 cases reported in the literature found that 38% had died with a mean age of death of 2 years. 32% were still alive at the time of the report with a mean age of 4.65. No data were available for the remainder. The author described living with DDS as "walking a multidimensional tight rope".

Medical treatment is designed primarily to address the secondary lymphedema part of the lipedema patient's condition. This treatment includes a course of manual lymphatic drainage and bandaging by a lymphedema therapist, followed by the wearing of custom-fitted compression garments or devices — usually stockings, and sometimes biker shorts and/or arm compression. Compression prevents recurrence of lymphedema, and in some lipedema patients can reduce the pain of lipedematous fat.

There is currently no known uniform medical procedure to cure lipedema. It is, however, successfully managed through a variety of consistently applied techniques to improve the health of the legs and prevent the condition from returning in more difficult to manage levels. Management involves reducing dietary sodium intake, frequent, gentle exercise to promote circulation in the legs, such as rebound exercise, and treatments typical for lymphedema treatment.

Juvenile nephronophthisis is the juvenile form of nephronophthisis that causes end stage renal disease around the age of 13; infantile nephronophthisis and adolescent nephronophthisis cause ESRD around the ages of 1 and 19, respectively.

The treatment for AME is based on the blood pressure control with Aldosterone antagonist like Spironalactone which also reverses the hypokalemic metabolic alkalosis and other anti-hypertensives. Renal transplant is found curative in almost all clinical cases.AME is exceedingly rare, with fewer than 100 cases recorded worldwide.

Liquorice consumption may also cause a temporary form of AME due to its ability to block 11β-hydroxysteroid dehydrogenase type 2, in turn causing increased levels of cortisol. Cessation of licorice consumption will reverse this form of AME.

Denys–Drash syndrome (DDS) or Drash syndrome is a rare disorder or syndrome characterized by gonadal dysgenesis, nephropathy, and Wilms' tumor.

Antiviral treatment has been tried with some success in a small number of patients.