In general, children with a small isolated nevus and a normal physical exam do not need further testing; treatment may include potential surgical removal of the nevus. If syndrome issues are suspected, neurological, ocular, and skeletal exams are important. Laboratory investigations may include serum and urine calcium and phosphate, and possibly liver and renal function tests. The choice of imaging studies depends on the suspected abnormalities and might include skeletal survey, CT scan of the head, MRI, and/or EEG.

Depending on the systems involved, an individual with Schimmelpenning syndrome may need to see an interdisciplinary team of specialists: dermatologist, neurologist, ophthalmologist, orthopedic surgeon, oral surgeon, plastic surgeon, psychologist.

If a patient displays congenital melanocytic nevi or giant congenital melanocytic nevi, the criteria for diagnosis of neurocutaneous melanosis is as follows:

- Melanocytic deposits exist within the central nervous system that are either malignant or benign

- The cutaneous lesions, giant or otherwise, are not malignant

This criteria is typically validated through biopsy of the cutaneous lesions and imaging of the central nervous system. It is important to establish that the cutaneous lesions are benign. If not, then the melanocytic deposits in the central nervous system may be the result of metastasis of cutaneous melanoma and not neurocutaneous melanosis.

Imaging has been shown to be the only reliable detection method for the presence of neurocutaneous melanosis that can be performed in living patients. Currently, the preferred imaging modality for diagnosis of neurocutaneous melanosis is Magnetic Resonance Imaging, although ultrasound is another viable option. The signal due melanin deposits in the leptomeninges typical of neurocutaneous melanosis can be easily detected in MRI scans of patients under four months old. In patients above this age, there is some suggestion that normal brain myelination may partially obscure these signals.

As most patients with neurocutaneous melanosis are asymptomatic, those who are diagnosed through MR imaging are not guarantied to develop symptoms. Those diagnosed who did not develop symptoms ranged from 10% to 68%. This wide range is most likely due to the large number of asymptomatic, undiagnosed patients with neurocutaneous melanosis.

Large and especially giant congenital nevi are at higher risk for malignancy degeneration into melanoma. Because of the premalignant potential, it is an acceptable clinical practice to remove congenital nevi electively in all patients and relieve the nevocytic overload.

The majority of patients with neurocutaneous melanosis are asymptomatic and therefore have a good prognosis with few complications. Most are not diagnosed, so definitive data in not available. For symptomatic patients, the prognosis is far worse. In patients without the presence of melanoma, more than 50% die within 3 years of displaying symptoms. While those with malignancy have a mortality rate of 77% with most patients displaying symptoms before the age of 2.

The presence of a Dandy-Walker malformation along with neurocutaneous melanosis, as occurs in 10% of symptomatic patients, further deteriorates prognosis. The median survival time for these patients is 6.5 months after becoming symptomatic.

Benign congenital nevi can have histological characteristics resembling melanomas, often breaking most if not all of the ABCDE rules. Dermatoscopic findings of the smaller forms of benign congenital nevi can aid in their differentiation from other pigmented neoplasms.

Microscopically, congenital melanocytic nevi appear similar to acquired nevi with two notable exceptions. For the congenital nevus, the neval cells are found deeper into the dermis. Also, the deeper nevus cells can be found along with neurovascular bundles, with both surrounding hair follicles, sebaceous glands, and subcutaneous fat. Such annexes and the hypodermis can also be hypoplasic or, conversely, present aspects of hamartoma.

Phakomatoses refers to a group of neuro-oculo-cutaneous syndromes or neurocutaneous disorders involving structures arising from the embryonic ectoderm. These multisystem disorders involve the ectodermal structures like central nervous system, skin and eyes. The lesions have a variable severity. However, it has been subsequently noted that mesodermal and endodermal tissues too are involved.

A number of genetic and acquired diseases come in this category and may affect one or more of these tissues. However, in some conditions, such as von Hippel-Lindau disease, ectodermal presentation is minimal.

The term, from the Greek φακός, "phakos", "spot, lens", suffix-(o)ma (-ωμα) and the suffix -osis, also called "Mother's spot" or "Birth mark" was introduced by Jan van der Hoeve in 1920, before the distinct genetic basis of each of these diseases was understood.

Conditions which may be confused with NF include, LEOPARD syndrome, and Legius syndrome.

Nevus sebaceous was first identified in 1895 by Jadassohn. Sebaceous nevi occur in 1 to 3 of 1000 births, with equal incidence by sex. There is no test to determine whether an individual born with a sebaceous nevus will go on to develop further symptoms of Schimmelpenning syndrome. It has been reported that up to 10% of individuals with epidermal nevi may develop additional syndrome symptoms, but that number appears to be inconsistent with the rarity of the syndrome and may be overstated. Prevalence is unknown, but Epidermal nevus syndrome is listed with the National Organization for Rare Disorders, which defines "rare" as affecting "fewer than 200,000 people in the United States."

CT and MRI are most often used to identify intracranial abnormalities. When a child is born with a facial cutaneous vascular malformation covering a portion of the upper or the lower eyelids, imaging should be performed to screen for intracranial leptomeningeal angiomatosis. The haemangioma present on the surface of the brain is in the vast majority of cases on the same side as the birth mark and gradually results in calcification of the underlying brain and atrophy of the affected region

Surgical removal of tumors is an option, however the risks involved should be assessed first. With regard to OPG (optic pathway gliomas), the preferred treatment is chemotherapy. However, radiotherapy isn't recommended in children who present with this disorder. It is recommended that children diagnosed with NF1 at an early age have an examination each year, which allows any potential growths or changes related to the disorder to be monitored.

Although it is possible for the birthmark and atrophy in the cerebral cortex to be present without symptoms, most infants will develop convulsive seizures during their first year of life. There is a greater likelihood of intellectual impairment when seizures are resistant to treatment. Studies do not support the widely held belief that seizure frequency early in life in patients who have SWS is a prognostic indicator.

Cutis laxa (also known as chalazoderma, dermatochalasia, dermatolysis, dermatomegaly, generalized elastolysis, generalized elastorrhexis, or pachydermatocele) is a group of rare connective tissue disorders in which the skin becomes inelastic and hangs loosely in folds.

Sjögren–Larsson syndrome (SLS) is an autosomal recessive form of ichthyosis apparent at birth.

Sjögren–Larsson syndrome is a rare autosomal, recessive, neurocutaneous disease. This disease can be identified by a triad of medical disorders. The first is ichthyosis, which is a buildup of skin to form a scale-like covering that causes dry skin and other problems. The second identifier is spastic paraplegia which is characterized by leg spasms. The final identifier is intellectual delay.

The gene of SLS is found on chromosome 17. In order for a child to receive SLS both parents must be carriers of the SLS gene. If they are carriers their child has a ¼ chance of getting the disease. In 1957 Sjogren and Larsson proposed that the Swedes with the disease all descended from a common ancestor 600 years ago. Today only 30–40 persons in Sweden have this disease.

It is associated with a deficiency of the enzyme "fatty aldehyde dehydrogenase". At least 11 distinct mutations have been identified.

In most cases, cutis laxa is inherited. Autosomal dominant, autosomal recessive, and X-linked recessive forms have been described, but acquired forms also occur.

Cutis laxa is associated with deficient or absent elastin fibers in the extracellular matrix. Various mutations in genes have been identified.

Cutis laxa may be caused by mutations in the genes: "ELN", "ATP6V0A2",

ATP7A, "FBLN4", "FBLN5", and "PYCR1". A related neurocutaneous syndrome may be caused by mutations in the gene "ALDH18A1" ("P5CS").

DNA repair defects are seen in nearly all of the diseases described as accelerated aging disease, in which various tissues, organs or systems of the human body age prematurely. Because the accelerated aging diseases display different aspects of aging, but never every aspect, they are often called segmental progerias by biogerontologists.

Some biogerontologists question that such a thing as "accelerated aging" actually exists, at least partly on the grounds that all of the so-called accelerated aging diseases are segmental progerias. Many disease conditions such as diabetes, high blood pressure, etc., are associated with increased mortality. Without reliable biomarkers of aging it is hard to support the claim that a disease condition represents more than accelerated mortality.

Against this position other biogerontologists argue that premature aging phenotypes are identifiable symptoms associated with mechanisms of molecular damage. The fact that these phenotypes are widely recognized justifies classification of the relevant diseases as "accelerated aging". Such conditions, it is argued, are readily distinguishable from genetic diseases associated with increased mortality, but not associated with an aging phenotype, such as cystic fibrosis and sickle cell anemia. It is further argued that segmental aging phenotype is a natural part of aging insofar as genetic variation leads to some people being more disposed than others to aging-associated diseases such as cancer and Alzheimer's disease.

Getting a regular eye exam may play a role in identifying the signs of some systemic diseases. "The eye is composed of many different types of tissue. This unique feature makes the eye susceptible to a wide variety of diseases as well as provides insights into many body systems. Almost any part of the eye can give important clues to the diagnosis of systemic diseases. Signs of a systemic disease may be evident on the outer surface of the eye (eyelids, conjunctiva and cornea), middle of the eye and at the back of the eye (retina)."

Since 500 B.C., some researchers have believed that the physical condition of the fingernails and toenails can indicate various systemic diseases. Careful examination of the fingernails and toenails may provide clues to underlying systemic diseases , since some diseases have been found to cause disruptions in the nail growth process. The nail plate is the hard keratin cover of the nail. The nail plate is generated by the nail matrix located just under the cuticle. As the nail grows, the area closest to becoming exposed to the outside world (distal) produces the deeper layers of the nail plate, while the part of the nail matrix deeper inside the finger (proximal) makes the superficial layers. Any disruption in this growth process can lead to an alteration in the shape and texture.

For example, pitting looks like depressions in the hard part of the nail. Pitting is to be associated with psoriasis, affecting 10% - 50% of patients with that disorder. Pitting also may be caused by a variety of systemic diseases, including reactive arthritis and other connective tissue disorders, sarcoidosis, pemphigus, alopecia areata, and incontinentia pigmenti. Because pitting is caused by defective layering of the superficial nail plate by the proximal nail matrix, any localized dermatitis (e.g., atopic dermatitis or chemical dermatitis) that disrupts orderly growth in that area also can cause pitting.

"Life-threatening disease redirects here".

A systemic disease is one that affects a number of organs and tissues, or affects the body as a whole.

Dozens of congenital metabolic diseases are now detectable by newborn screening tests, especially the expanded testing using mass spectrometry. This is an increasingly common way for the diagnosis to be made and sometimes results in earlier treatment and a better outcome. There is a revolutionary Gas chromatography–mass spectrometry-based technology with an integrated analytics system, which has now made it possible to test a newborn for over 100 mm genetic metabolic disorders.

Because of the multiplicity of conditions, many different diagnostic tests are used for screening. An abnormal result is often followed by a subsequent "definitive test" to confirm the suspected diagnosis.

Common screening tests used in the last sixty years:

- Ferric chloride test (turned colors in reaction to various abnormal metabolites in urine)

- Ninhydrin paper chromatography (detected abnormal amino acid patterns)

- Guthrie bacterial inhibition assay (detected a few amino acids in excessive amounts in blood) The dried blood spot can be used for multianalyte testing using Tandem Mass Spectrometry (MS/MS). This given an indication for a disorder. The same has to be further confirmed by enzyme assays, IEX-Ninhydrin, GC/MS or DNA Testing.

- Quantitative measurement of amino acids in plasma and urine

- IEX-Ninhydrin post column derivitization liquid ion-exchange chromatography (detected abnormal amino acid patterns and quantitative analysis)

- Urine organic acid analysis by gas chromatography–mass spectrometry

- Plasma acylcarnitines analysis by mass spectrometry

- Urine purines and pyrimidines analysis by gas chromatography-mass spectrometry

Specific diagnostic tests (or focused screening for a small set of disorders):

- Tissue biopsy or necropsy: liver, muscle, brain, bone marrow

- Skin biopsy and fibroblast cultivation for specific enzyme testing

- Specific DNA testing

A 2015 review reported that even with all these diagnostic tests, there are cases when "biochemical testing, gene sequencing, and enzymatic testing can neither confirm nor rule out an IEM, resulting in the need to rely on the patient's clinical course."

Diagnostic procedures that may reveal muscular disorders include direct clinical observations. This usually starts with the observation of bulk, possible atrophy or loss of muscle tone. Neuromuscular disease can also be diagnosed by testing the levels of various chemicals and antigens in the blood, and using electrodiagnostic medicine tests including electromyography (measuring electrical activity in muscles) and nerve conduction studies.

In neuromuscular disease evaluation, it is important to perform musculoskeletal and neurologic examinations. Genetic testing is an important part of diagnosing inherited neuromuscular conditions.

"The phenotypic parameters that define a ciliopathy may be used to both recognize the cellular basis of a number of genetic disorders and to facilitate the diagnosis and treatment of some diseases of unknown" cause.

Rare diseases are usually genetic and are therefore chronic. EURORDIS estimates that at least 80% of them have identified genetic origins. Other rare diseases are the result of infections and allergies or due to degenerative and proliferative causes.

Symptoms of some rare diseases may appear at birth or in childhood, whereas others only appear once adulthood is reached.

Research publications emphasize rare diseases that are chronic or incurable, although many short-term medical conditions are also rare diseases.

One cause of the White Dot Syndromes as suggested by Gass involves viral or infectious agents. Specifically pertaining to the ‘AZOOR complex,’ Gass has postulated that a virus may enter the retina at the optic head and the infection may spread from one photoreceptor to another. Some unexplained features include the development of more than one disease in the same patient and the majority of cases occurring in females.

According to Becker’s common genetic hypothesis, “unlike mendelian genetic disorders, common autoimmune and inflammatory diseases arise from combinatorial interactions of common non-disease specific loci, disease specific loci, and specific environmental triggers.” An important aspect of this hypothesis pertains to the existence of common non-disease genes that predispose patients to autoimmune diseases. Jampol and Becker insinuate that ‘common susceptibility genes’ are present in patients affected by white dot syndromes. The presence of environmental triggers, such as viral infections, immunizations, and stress, and interactions with other genes contribute to the development of the white dot syndromes. Additionally, Jampol and Becker hypothesize that the predisposing genetic loci can be identified.

Gass points to a lack of evidence in support of the Becker theory. Instead, Gass highlights that although evidence indicates that patients with AZOOR have a greater chance of developing autoimmune diseases, this does not mean that the AZOOR complex of disorders are themselves autoimmune diseases. This is supported by the difficulty in detecting “retinal autoantibodies” in AZOOR patients.

Two other diseases which also present with white dots on the fundus are retinitis punctata albescens and fundus albipunctatus. These diseases are not white dot syndromes, but have much more defined etiology. Retinitis punctata albescens is caused by mutations in RLBP1, the gene for retinaldehyde binding protein 1. In comparison, fundus albipunctatus is caused by mutations in RDH5 gene for an 11-cis-RDH in RPE cells.