Diagnosis of mesoblastic nephroma and its particular type (i.e. classic, mixed, or cellular) is made by histological examination of tissues obtained at surgery. Besides its histological appearance, various features of this disease aid in making a differential diagnosis that distinguish it from the following childhood neoplasms:

- Wilm's tumor is the most common childhood kidney neoplasm, representing some 85% of cases. Unlike mesoblastic nephroma, 3 years of age. Bilateral kidney tumors, concurrent birth defects, and/or metastatic disease at presentation favor a diagnosis of Wilm's tumor.

- congenital infantile sarcoma is a rare aggressive sarcoma typically presenting in the lower extremities, head, or neck of infants during their first year of life. The histology, association with the "ETV6-NRTK3" fusion gene along with certain chromosome trisomies, and the distribution of markers for cell type (i.e. cyclin D1 and Beta-catenin) within this tumor are the same as those found in cellular mesoblastic nephroma. Mesoblastic nephroma and congenital infantile sarcoma appear to be the same diseases with mesoblastic lymphoma originating in the kidney and congenital infantile sarcoma originating in non-renal tissues.

- Rhabdoid tumor, which accounts for 5-510% of childhood kidney neoplasms, occurs predominantly in children from 1 to 2 years of age. Unlike mesoblastic nephroma, rhabdoid tumors may present with tumors in other tissues including in ~13% of cases, the brain. Rhabdoid tumors have a distinctive histology and abnormalities (i.e. loss of heterozygosity, single nucleotide polymorphism, and deletions) in chromosome 22.

- Clear cell sarcoma of the kidney, which is responsible for 5-10% of childhood pediatric tumors, occurs predominantly in children from 2 to 3 years of age. Unlike meoblastic nephorma, clear cell sarcoma of the kidney presents with metastasis, particularly to bone, in 5-6% of cases; it histology is diverse and has been mistaken for mesoblastic nephroma. One chromosomal translocations t,(10;17)(q22;p13), has been repeatedly reported to be associated with clear cell sarcoma of the kidney.

- Infantile myofibromatosis is a fibrous tumor of infancy and childhood most commonly presenting during the first 2 years of life as a single subcutaneous nodule of the head and neck region or less commonly as multiple lesions of skin, muscle, bone, and in ~33% of these latter cases, visceral organs. All of these lesions have an excellent prognosis and can regress spontaneously except for those in which there is visceral involvement where the prognosis is poor. While infantile myofibromatosis and classic mesoblastic nephroma have been suggested to be the same diseases because of their very similar histology, studies on the distribution of cell-type markers (i.e. cyclin D1 and Beta-catenin) indicate that they have different cellular origins.

Based on a survey of >800, surgical removal of the entire involved kidney plus the peri-renal fat appeared curative for the majority of all types of mesoblastic nephroma; the patient overall survival rate was 94%. Of the 4% of non-survivors, half were due to surgical or chemotherapeutic treatments. Another 4% of these patients suffered relapses, primarily in the local area of surgery rare cases of relapse due to lung or bone metastasis.. About 60% of these recurrent cases had a complete remission following further treatment. Recurrent disease was treated with a second surgery, radiation, and/or chemotherapy that often vincristine and actinomycin treatment. Removal of the entire afflicted kidney plus the peri-renal fat appears critical to avoiding local recurrences. In general, patients who were older than 3 months of age at diagnosis or had the cellular form of the disease, stage III disease, or involvement of renal lymph nodes had a higher recurrence rate. Among patients with these risk factors, only those with lymph node involvement are recommended for further therapy.

It has been suggested that mesoblastic nephroma patients with lymph node involvement or recurrent disease might benefit by adding the ALK inhibitor, crizotinib, or a tyrosine kinase inhibitor, either larotrectinib or entrectinib, to surgical, radiation, and/or chemotherapy treatment regimens. These drugs inhibit NTRK3's tyrosine kinase activity. Crizotinib has proven useful in treating certain cases of acute lymphoblastic leukemia that are associated with the "ETV6-NTRK3" fusion gene while larotrectinib and entrectinib have been useful in treating various cancers (e.g. a metastatic sarcoma, papillary thyroid cancer, non-small-cell lung carcinoma, gastrointestinal stromal tumor, mammary analog secretory carcinoma, and colorectal cancer) that are driven by mutated, overly active tyrosine kinases. Relevant to this issue, a 16-month-old girl with infantile fibrosarcoma harboring the "ETV6–NTRK3" fusion gene was successfully trated with larotrectinib. The success of these drugs, howwever, will likely depend on the relative malignancy-promoting roles of ETV6-NTRK3 protein's tyrosine kinase activity, the lose of ETV6-related transcription activity accompanying formation of ETV6-NTRK3 protein, and the various trisomy chromosomes that populate mesoblastic nephroma.

Cystic nephromas are diagnosed by biopsy or excision. It is important to correctly diagnose them as, radiologically, they may mimic the appearance of a renal cell carcinoma that is cystic.

Ancillary testing for fibrosarcoma includes IHC, where vimentin is positive, cytokeratin and S100 are negative, and actin is variable.

Fibrosarcoma occurs most frequently in the mouth in dogs . The tumor is locally invasive, and often recurs following surgery . Radiation therapy and chemotherapy are also used in treatment. Fibrosarcoma is also a rare bone tumor in dogs.

In cats, fibrosarcoma occurs on the skin. It is also the most common vaccine-associated sarcoma. In 2014, Merial launched Oncept IL-2 in Europe for the management of such feline fibrosarcomas.

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.

Most children (>80%) with BWS do not develop cancer; however, children with BWS are much more likely (~600 times more) than other children to develop certain childhood cancers, particularly Wilms' tumor (nephroblastoma), pancreatoblastoma and hepatoblastoma. Individuals with BWS appear to only be at increased risk for cancer during childhood (especially before age four) and do not have an increased risk of developing cancer in adulthood. If 100 children with BWS were followed from birth until age ten, about 10 cases of cancer would be expected in the group before age four, and about 1 case of cancer in the group would be expected between age four and ten.

In addition to Wilms tumor and hepatoblastoma, children with BWS have been shown in individual case reports to develop ganglioneuroma, adrenocortical carcinoma, acute lymphoid leukemia, liver sarcoma, thyroid carcinoma, melanoma, rhabdomyosarcoma, and mesoblastic nephroma.

Wilms tumor, hepatoblastoma, and mesoblastic nephroma can usually be cured if diagnosed early. Early diagnosis allows physicians to treat the cancer when it is at an early stage. In addition, there is less toxic treatment. Given the importance of early diagnosis, all children with BWS should receive cancer screening.

An abdominal ultrasound every 3 months until at least eight years of age is recommended and a blood test to measure alpha-fetoprotein (AFP) every 6 weeks until at least four years of age. Families and physicians should determine screening schedules for specific patients, especially the age at which to discontinue screening, based upon their own evaluation of the risk-benefit ratio.

Cystic nephromas are often asymptomatic. They are typically discovered on medical imaging incidentally (i.e. an incidentaloma).

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.

Abdominal wall defects are common in newborns with BWS and may require surgical treatment. These defects can range in severity from omphalocele (most serious) to umbilical hernia and diastasis recti (least serious). An "omphalocele" is a congenital malformation in which a newborn's intestines, and sometimes other abdominal organs, protrude out of the abdomen through the umbilicus. Newborns with an omphalocele typically require surgery to place the abdominal contents back into the abdomen in order to prevent serious infection or shock. An "umbilical hernia" is also a defect in which abdominal contents come through weak abdominal wall muscle at the umbilicus. In general, newborns with umbilical hernias do not require treatment because often these hernias spontaneously close by age four. If, after this time, a hernia is still present, surgery may be recommended. "Diastasis recti" is a separation of the left and right sides of the rectus abdominis muscle that are normally joined together. Children with diastasis recti usually require no treatment because the condition resolves as the child grows.

Neonatal hypoglycemia, low blood glucose in the first month of life, occurs in about half of children with BWS. Most of these hypoglycemic newborns are asymptomatic and have a normal blood glucose level within days. However, untreated persistent hypoglycemia can lead to permanent brain damage. Hypoglycemia in newborns with BWS should be managed according to standard protocols for treating neonatal hypoglycemia. Usually this hypoglycemia can easily be treated with more frequent feedings or medical doses of glucose. Rarely (<5%) children with BWS will continue to have hypoglycemia after the neonatal period and require more intensive treatment. Such children may require tube feedings, oral hyperglycemic medicines, or a partial pancreatectomy.

Macroglossia, a large tongue, is a very common (>90%) and prominent feature of BWS. Infants with BWS and macroglossia typically cannot fully close their mouth in front of their large tongue, causing it to protrude out. Macroglossia in BWS becomes less noticeable with age and often requires no treatment; but it does cause problems for some children with BWS. In severe cases, macroglossia can cause respiratory, feeding, and speech difficulties. Children with BWS and significant macroglossia should be evaluated by a craniofacial team.

The best time to perform surgery for a large tongue is not known. Some surgeons recommend performing the surgery between 3 and 6 months of age. Surgery for macroglossia involves removing a small part of the tongue so that it fits within the mouth to allow for proper jaw and tooth development.

Nevus flammeus (port-wine stain) is a flat, red birthmark caused by a capillary (small blood vessel) malformation. Children with BWS often have nevus flammeus on their forehead or the back of their neck. Nevus flammeus is benign and commonly does not require any treatment.

Hemihypertrophy (hemihyperplasia) is an abnormal asymmetry between the left and right sides of the body occurring when one part of the body grows faster than normal. Children with BWS and hemihypertrophy can have an isolated asymmetry of one body part, or they can have a difference affecting the entire one side of the body. Individuals who do not have BWS can also have hemihypertrophy. Isolated hemihypertrophy is associated with a higher risk for cancer. The types of cancer and age of the cancers are similar to children with BWS. As a result, children with hemihypertrophy should follow the general cancer screening protocol for BWS.

Hemihypertrophy can also cause various orthopedic problems, so children with significant limb hemihyperplasia should be evaluated and followed by an orthopedic surgeon.

Hemihyperplasia affecting the face can sometimes cause significant cosmetic concerns that may be addressed by a cranial facial team.

Neurocristopathy is a diverse class of pathologies that may arise from defects in the development of tissues containing cells commonly derived from the embryonic neural crest cell lineage. The term was coined by Robert P. Bolande in 1974.

Accepted examples are piebaldism, Waardenburg syndrome, Hirschsprung disease, Ondine's curse (congenital central hypoventilation syndrome), pheochromocytoma, paraganglioma, Merkel cell carcinoma, multiple endocrine neoplasia, neurofibromatosis type I, CHARGE syndrome, familial dysautonomia, DiGeorge syndrome, Axenfeld-Rieger syndrome, Goldenhar syndrome (a.k.a. hemifacial microsomia), craniofrontonasal syndrome, congenital melanocytic nevus, melanoma, and certain congenital heart defects of the outflow tract, in particular.

Multiple sclerosis has also been suggested as being neurocristopathic in origin.

The usefulness of the definition resides in its ability to refer to a potentially common etiological factor for certain neoplasms and/or congenital malformation associations that are otherwise difficult to group with other means of nosology.

MASC is currently treated as a low-grade (i.e. Grade 1) carcinoma with an overall favorable prognosis. These cases are treated by complete surgical excision. However, the tumor does have the potential to recur locally and/or spread beyond surgically dissectible margins as well as metastasize to regional lymph nodes and distant tissues, particularly in tumors with histological features indicating a high cell growth rate potential. One study found lymph node metastasis in 5 of 34 MASC patients at initial surgery for the disease; these cases, when evidencing no further spread of disease, may be treated with radiation therapy. The treatment of cases with disease spreading beyond regional lymph nodes has been variable, ranging from simple excision to radical resections accompanied by adjuvant radiotherapy and/or chemotherapy, depending on the location of disease. Mean disease-free survival for MASC patients has been reported to be 92 months in one study.

The tyrosine kinase activity of NTRK3 as well as the ETV6-NTRK3 protein is inhibited by certain tyrosine kinase inhibitory drugs such as Entrectinib and LOXO-101; this offers a potential medical intervention method using these drugs to treat aggressive MASC disease. Indeed, one patient with extensive head and neck MASC disease obtained an 89% fall in tumor size when treated with entrectinib. This suppression lasted only 7 months due to the tumor's acquirement of a mutation in the "ETV6-NTRK3" gene. The newly mutated gene encoded an entrectinib-reisistant "ETV6-NTRK3" protein. Treatment of aggressive forms of MASC with NTRK3-inhibiting tyrosine kinase inhibiting drugs, perhaps with switching to another type of tyrosine kinase inhibitor drug if the tumor acquires resistance to the initial drug, is under study.STARTRK-2

A 2007 study followed 112 individuals for a mean of 12 years (mean age 25.3, range 12–71). No patient died during follow-up, but several required medical interventions. The mean final heights were 167 and 153 cm for men and women, respectively, which is approximately 2 standard deviations below normal.

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.

Infantile myofibromatosis (also known as "Congenital generalized fibromatosis," and "Congenital multicentric fibromatosis") is the most common fibrous tumor of infancy, in which eighty percent of patients have solitary lesions with half of these occurring on the head and neck, and 60% are present at or soon after birth. Less commonly, infantile myofibromatosis presents as multiple lesions of skin, muscle, and bone with about 1/3 of these cases also having lesions in their visceral organs. All of these cases have an excellent prognosis with their tumors sometimes regressing spontaneously except for those cases in which there is visceral involvement where the prognosis is poor. Infantile myofibromatosis and the classic form of mesoblastic nephroma have been suggested to be the same disease because of their very similar histology. However, studies on the distribution of cell-type markers (i.e. cyclin D1 and Beta-catenin) indicate that the two neoplasms likely have different cellular origins.

NS can be confirmed genetically by the presence of any of the known mutations listed above. However, despite identification of fourteen causative genes, the absence of a known mutation will not exclude the diagnosis, as there are more, as-yet-undiscovered genes that cause NS. Thus, the diagnosis of NS is still based on clinical features. In other words, it is made when a physician feels that a patient has enough of the features to warrant the label. The principal values of making a genetic diagnosis are that it guides additional medical and developmental evaluations, it excludes other possible explanations for the features, and it allows more accurate recurrence risk estimates. With more genotype-phenotype correlation studies being performed, a positive genetic diagnosis will help the clinician to be aware of possible anomalies specific to that certain gene mutation. For example, there is an increase in hypertrophic cardiomyopathy in patients with a mutation of "KRAS" and an increased risk of juvenile myelomonocytic leukemia for a mutation of "PTPN11". In the future, studies may lead to a targeted management of NS symptoms that depends on what genetic mutation a patient has.

Radiologic diagnosis

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.

Mammary analogue secretory carcinoma occurs somewhat more commonly in men (male to female ratio of <1.5:1.0). Patients with this disease have a mean age of 46 years although ~12% of cases occur in pediatric patients. Individuals typically present with symptomless tumors in the [[parotid|parotid salivary gland]] (68%), [[Oral mucosa#classification|buccal mucosa salivary glands]] (9%), [[Submandibular gland|submandibular salivary gland]] (8%) or in the small salivary glands of the lower lip (5%), upper lip (4%), and [[hard palate]] (4%). [[Histologically]], these tumors are described as have a morphology similar to secretory breast carcinoma; they typically having one or more of the following histological patterns: microcystic, papillary-cystic, follicular, and/or solid lobular. Other histological features of these tissues include: the presence of eosinophilic secretions as detected by staining strongly for [[eosin Y]]; positive staining with [[periodic acid-Schiff stain]] (often after [[diastase]]); the presence of vesicular oval nuclei with a single small but prominent [[nucleolus]]; and the absence of basophilic [[Haematoxylin]] or [[zymogen]] granules (i.e. vesicles that store enzymes near the cell's plasma membrane).

The cited histology features are insufficient to distinguish MASC from other [[Salivary gland neoplasm]]s such as [[acinic cell carcinoma]], low-grade cribriform cystadenocarcinoma, and adenocarcinoma not otherwise specified. MASC can be distinguished from these and other histologically similar tumors by either tissue identification of a) the "ETV6-NTRK3" fusion gene using [[Fluorescence in situ hybridization]] or [[reverse transcription polymerase chain reaction]] gene detection methods or b) a specific pattern of marker proteins as registered using specific antibody-based detection methods, i.e. MASC tissue should have detectable [[S100 protein|S100]] (a family of calcium binding proteins), [[Mammaglobin]] (a breast cancer marker, Keratin 7 (an intermediate filament found in epithelial cells), GATA3 (a transcription factor and breast cancer biomarker), SOX10 (a transcription factor important in neural crest origin cells and development of the peripheral nervous system), and STAT5A (a transcription factor) but lack antibody-detectable TP63 (a transcription factor in the same family as p53) and Anoctamin-1 (a voltage sensitive calcium activated chloride channel).

CCD may be detectable on prenatal ultrasound. After birth, signs in affected babies typically are abdominal distension, visible peristalsis, and watery stools persistent from birth that show chloride loss of more than 90 mmol/l.

An important feature in this diarrhea that helps in the diagnosis, is that it is the only type of diarrhea that causes metabolic alkalosis rather than metabolic acidosis.

Medical diagnosis of pulmonary hypoplasia in utero may use imaging, usually ultrasound or MRI. The extent of hypoplasia is a very important prognostic factor. One study of 147 fetuses (49 normal, 98 with abnormalities) found that a simple measurement, the ratio of chest length to trunk (torso) length, was a useful predictor of postnatal respiratory distress. In a study of 23 fetuses, subtle differences seen on MRIs of the lungs were informative. In a study of 29 fetuses with suspected pulmonary hypoplasia, the group that responded to maternal oxygenation had a more favorable outcome.

Pulmonary hypoplasia is diagnosed also clinically.

In the developed world, nearly all cases of congenital hypothyroidism are detected by the newborn screening program. These are based on measurement of TSH or thyroxine (T) on the second or third day of life (Heel prick).

If the TSH is high, or the T low, the infant's doctor and parents are called and a referral to a pediatric endocrinologist is recommended to confirm the diagnosis and initiate treatment. Often a technetium (Tc-99m pertechnetate) thyroid scan is performed to detect a structurally abnormal gland. A radioactive iodine (RAIU) exam will help differentiate congenital absence or a defect in organification (a process necessary to make thyroid hormone).

Smith Martin Dodd syndrome is a very rare genetic disorder first described by Smith et al. in 1994. It is characterized by small eyes, a diaphragmatic hernia, and Tetralogy of Fallot, a congenital heart defect. The only known case is of a 9-year-old boy with several congenital anomalies including a diaphragmatic hernia, microphthalmia, and Tetralogy of Fallot. It was found that the boy had a reciprocal translocation t(1;15)(q41;q21.2). A congenital diaphragmatic hernia is consistent with chromosome 1q41-q42 deletion syndrome, and the report by Smith et al. suggested that genes involved in the translocation may be important for the development of morphological characteristics, especially those of the eye or heart.

An absolute neutrophil count (ANC) chronically less than 500/mm3, usually less than 200/mm3, is the main sign of Kostmann's. Other elements include the severity of neutropenia, the chronology (from birth; not emerging later), and other normal findings (hemoglobin, platelets, general body health). Isolated neutropenia in infants can occur in viral infections, autoimmune neutropenia of infancy, bone marrow suppression from a drug or toxin, hypersplenism, and passive placental transfer of maternal IgG.

A bone marrow test can assist in diagnosis. The bone marrow usually shows early granulocyte precursors, but myelopoietic development stops ("arrests") at the promyelocyte and/or myelocyte stage, so that few maturing forms are seen. Neutrophil survival is normal.

Needs mention of (rarer) myelokathexis types. e.g. G6PC3 variant and

Most children born with congenital hypothyroidism and correctly treated with thyroxine grow and develop normally in all respects. Even most of those with athyreosis and undetectable T levels at birth develop with normal intelligence, although as a population academic performance tends to be below that of siblings and mild learning problems occur in some.

Congenital hypothyroidism is the most common preventable cause of intellectual disability. Few treatments in the practice of medicine provide as large a benefit for as small an effort.

The developmental quotient (DQ, as per Gesell Developmental Schedules) of children with hypothyroidism at age 24 months that have received treatment within the first 3 weeks of birth is summarised below:

A low socioeconomic status in a deprived neighborhood may include exposure to “environmental stressors and risk factors.” Socioeconomic inequalities are commonly measured by the Cartairs-Morris score, Index of Multiple Deprivation, Townsend deprivation index, and the Jarman score. The Jarman score, for example, considers “unemployment, overcrowding, single parents, under-fives, elderly living alone, ethnicity, low social class and residential mobility.” In Vos’ meta-analysis these indices are used to view the effect of low SES neighborhoods on maternal health. In the meta-analysis, data from individual studies were collected from 1985 up until 2008. Vos concludes that a correlation exists between prenatal adversities and deprived neighborhoods. Other studies have shown that low SES is closely associated with the development of the fetus in utero and growth retardation. Studies also suggest that children born in low SES families are “likely to be born prematurely, at low birth weight, or with asphyxia, a birth defect, a disability, fetal alcohol syndrome, or AIDS.” Bradley and Corwyn also suggest that congenital disorders arise from the mother’s lack of nutrition, a poor lifestyle, maternal substance abuse and “living in a neighborhood that contains hazards affecting fetal development (toxic waste dumps).” In a meta-analysis that viewed how inequalities influenced maternal health, it was suggested that deprived neighborhoods often promoted behaviors such as smoking, drug and alcohol use. After controlling for socioeconomic factors and ethnicity, several individual studies demonstrated an association with outcomes such as perinatal mortality and preterm birth.