The diagnostic process typically begins with a medical history workup followed by a medical examination by a physician. Imaging tests, such as CT scans and MRIs, help provide a clearer picture. The physician typically looks for fluid (or other bodily substance) filled sacs to appear in the scans, as is shown in the CT scan of a colloid cyst. A primary health care provider will refer an individual to a neurologist or neurosurgeon for further examination. Other diagnostic methods include radiological examinations and macroscopic examinations. After a diagnosis has been made, immunohistochemistry may be used to differentiate between epithelial cysts and arachnoid cysts. These examinations are useful to get a general idea of possible treatment options, but can be unsatisfactory to diagnose CNS cysts. Professionals still do not fully understand how cysts form; however, analyzing the walls of different cyst types, using electron microscopes and light microscopes, has proven to be the best diagnostic tool. This has led to more accurate cyst classification and correct course of action for treatments that are cyst specific. In the past, before imaging scans or tests were available, medical professionals could only diagnose cysts via exploratory surgery.

Although often described as benign, a teratoma does have malignant potential. In a UK study of 351 infants and children diagnosed with "benign" teratoma reported 227 with MT, 124 with IT. Five years after surgery, event-free survival was 92.2% and 85.9%, respectively, and overall survival was 99% and 95.1%. A similar study in Italy reported on 183 infants and children diagnosed with teratoma. At 10 years after surgery, event free and overall survival were 90.4% and 98%, respectively.

Depending on which tissue(s) it contains, a teratoma may secrete a variety of chemicals with systemic effects. Some teratomas secrete the "pregnancy hormone" human chorionic gonadotropin (βhCG), which can be used in clinical practice to monitor the successful treatment or relapse in patients with a known HCG-secreting teratoma. This hormone is not recommended as a diagnostic marker, because most teratomas do not secrete it. Some teratomas secrete thyroxine, in some cases to such a degree that it can lead to clinical hyperthyroidism in the patient. Of special concern is the secretion of alpha-fetoprotein (AFP); under some circumstances AFP can be used as a diagnostic marker specific for the presence of yolk sac cells within the teratoma. These cells can develop into a frankly malignant tumor known as yolk sac tumor or endodermal sinus tumor.

Adequate follow-up requires close observation, involving repeated physical examination, scanning (ultrasound, MRI, or CT), and measurement of AFP and/or βhCG.

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.

Imaging studies are performed before surgery or biopsy to preclude an intracranial connection. Images usually show a sharply circumscribed but expansile mass. It may be difficult to exclude the intracranial connection if the defect is small whether employing computed tomography or magnetic resonnance.

Extraspinal ependymoma, usually considered to be a glioma (a type of non-germ cell tumor), may be an unusual form of mature teratoma.

SCTs are very rare in adults, and as a rule these tumors are benign and have extremely low potential for malignancy. This estimation of potential is based on the idea that because the tumor existed for decades prior to diagnosis, without becoming malignant, it has little or no potential to ever become malignant. For this reason, and because coccygectomy in adults has greater risks than in babies, some surgeons prefer not to remove the coccyx of adult survivors of SCT. There are case reports of good outcomes.

Management of most fetal SCTs involves watchful waiting prior to any treatment. An often used decision tree is as follows:

- Perform detailed ultrasound exam including fetal echocardiogram and Doppler flow analysis

- If fetal high output failure, placentomegaly, or hydrops

- If fetus not mature, perform pregnancy termination or fetal intervention

- Else fetus mature, perform emergency Cesarean section

- Else no emergent problems, perform serial non-stress tests and ultrasound biophysical profiles and plan delivery, as follows

- If emergent problems develop, return to top of decision tree

- Else if SCT over 5–10 cm or polyhydramnios, perform early (37 weeks gestation) elective Cesarean section

- Else SCT small and no complications, permit term spontaneous vaginal delivery

Emergent problems include maternal mirror syndrome, polyhydramnios, and preterm labor. Poor management decisions, including interventions that are either premature or delayed, can have dire consequences. A very small retrospective study of 9 babies with SCTs greater than 10 cm diameter reported slightly higher survivorship in babies remaining in utero slightly longer.

In many cases, a fetus with a small SCT (under 5 or 10 cm) may be delivered vaginally. Prior to the advent of prenatal detection and hence scheduled C-section, 90% of babies diagnosed with SCT were born full term.

The most common missed lesion is within the nasal cavity, where a fibrosed nasal polyp may be considered. However, it does not have glial tissue. Further, a polyp usually has mucoserous glands. The lesion is frequently misintrepreted as scar in the subcutaneous tissues, but scar in a <2 year old child would be uncommon. Special stains are frequently required to highlight the diagnosis.

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.

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.

The primary diagnosis is made with a computed tomography scan (CT scan). On a scan, hemangioblastoma shows as a well-defined, low attenuation region in the posterior fossa with an enhancing nodule on the wall. Sometimes multiple lesions are present.

A neurosurgeon performs a craniotomy as a means of entry to access the cyst. The cyst is then opened to release its contents, which are reabsorbed by the brain. This is commonly used with inflammatory cysts located in the ventricles, and can result in increased ventricular fluid flow within the brain.

Treatment for dermoid cyst is complete surgical removal, preferably in one piece and without any spillage of cyst contents. Marsupialization, a surgical technique often used to treat pilonidal cyst, is inappropriate for dermoid cyst due to the risk of malignancy.

The association of dermoid cysts with pregnancy has been increasingly reported. They usually present the dilemma of weighing the risks of surgery and anesthesia versus the risks of untreated adnexal mass. Most references state that it is more feasible to treat bilateral dermoid cysts of the ovaries discovered during pregnancy if they grow beyond 6 cm in diameter.

A small dermoid cyst on the coccyx can be difficult to distinguish from a pilonidal cyst. This is partly because both can be full of hair. A pilonidal cyst is a pilonidal sinus that is obstructed. Any teratoma near the body surface may develop a sinus or a fistula, or even a cluster of these. Such is the case of Canadian Football League linebacker Tyrone Jones, whose teratoma was discovered when he blew a tooth out of his nose.

The outcome for hemangioblastoma is very good, if surgical extraction of the tumor can be achieved; excision is possible in most cases and permanent neurologic deficit is uncommon and can be avoided altogether if the tumor is diagnosed and treated early. Persons with VHL syndrome have a bleaker prognosis than those who have sporadic tumors since those with VHL syndrome usually have more than one lesion.

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 MYD88 L2659 is a gene mutation found in the majority of WM cases. During CSF analysis, PCR amplification of genomic DNA found in the fluid, followed by sequencing, can determine if the mutation is present within the CNS; if so, this would be indicative of, though not conclusive, of BNS.

MRI with gadolinium contrast is the primary radiologic tool used to diagnose ailments of the central nervous system, BNS included. MRI’s effect is twofold in that it is able to identify brain and spine abnormalities, as well as identifying tissues appropriate for biopsy. MRI with gadolinium contrast can also discern which form of BNS has formed. Where the tumoral form of BNS is highlighted by tumor growth in the subcortical hemispheric regions, the diffuse form of BNS is characterized by leptomeningeal and perivascular infiltration by lymphoid cells. Other characteristics of BNS identified via MRI are abnormal enhancement of cranial and spinal nerves, as well as thickening and enhancement of the cauda equina.

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.

The histology of EST is variable, but usually includes malignant endodermal cells. These cells secrete alpha-fetoprotein (AFP), which can be detected in tumor tissue, serum, cerebrospinal fluid, urine and, in the rare case of fetal EST, in amniotic fluid. When there is incongruence between biopsy and AFP test results for EST, the result indicating presence of EST dictates treatment. This is because EST often occurs as small "malignant foci" within a larger tumor, usually teratoma, and biopsy is a sampling method; biopsy of the tumor may reveal only teratoma, whereas elevated AFP reveals that EST is also present. GATA-4, a transcription factor, also may be useful in the diagnosis of EST.

Diagnosis of EST in pregnant women and in infants is complicated by the extremely high levels of AFP in those two groups. Tumor surveillance by monitoring AFP requires accurate correction for gestational age in pregnant women, and age in infants. In pregnant women, this can be achieved simply by testing maternal serum AFP rather than tumor marker AFP. In infants, the tumor marker test is used, but must be interpreted using a reference table or graph of normal AFP in infants.

EST can have a multitude of morphologic patterns including: reticular, endodermal sinus-like, microcystic, papillary, solid, glandular, alveolar, polyvesicular vitelline, enteric and hepatoid.

Schiller-Duval bodies on histology are pathognomonic and seen in the context of the endodermal sinus-like pattern.

Definitive diagnosis can only occur with positive identification of the larvae. This involves radiologic imaging (preferably MRI which can reveal larval migration tracks and in some cases the larvae themselves) as well as surgical exploration during which larvae can be removed and examined for identification. Identification of exact species is often impossible as the instars of the various "Cuterebra" and "Trychoderma" spp. exhibit significant resemblance, but identification as a "Cuterebra" bot fly is sufficient for diagnosis as cuterebriasis. Typically, a third larval instar is found and identifiable by its dark, thick, heavily spined body.

Most fetuses with triploidy do not survive to birth, and those that do usually pass within days. As there is no treatment for Triploidy, palliative care is given if a baby survives to birth. If Triploidy is diagnosed during the pregnancy, termination is often offered as an option due to the additional health risks for the mother (preeclampsia, a life-threatening condition, or choriocarcinoma, a type of cancer). Should a mother decide to carry until term or until a spontaneous miscarriage occurs, doctors will monitor her closely in case either condition develops.

Mosaic triploidy has an improved prognosis, but affected individuals have moderate to severe cognitive disabilities.

The disorder is an autosomal dominant genetic trait caused by a mutation in the HLXB9 homeobox gene. In 2000 the first large series of Currarino cases was genetically screened for HLXB9 mutations, and it was shown that the gene is specifically causative for the syndrome, but not for other forms of sacral agenesis. The study was published on the American Journal of Human Genetics.

The administration of immunotherapy, in association with chemotherapy or tumor removal, .