GCNIS is seen in the following settings:

- Almost all invasive germ cell tumours of the testis in adults

- Fifty percent of patients with GCNIS developed invasive germ cell tumours within five years of initial diagnosis.

- Five percent of contralateral testes in men with a history of prior testicular germ cell tumour.

- Less than five percent of cryptorchid testes.

- Less than one percent of patients with infertility.

Not all germ cell tumors (GCTs) arise from "intratubular germ cell neoplasia". The following testicular GCTs do not arise from ITGCN:

- Spermatocytic seminoma

- Pediatric Yolk sac tumors (endodermal sinus tumour). This is currently an area of controversy as some authors dispute the absence of ITGCN in these cases.

- Teratoma (rare exceptions)

Despite their name, germ cell tumors occur both within and outside the ovary and testis.

- head

- inside the cranium — pineal and suprasellar locations are most commonly reported

- inside the mouth — a fairly common location for teratoma

- neck

- mediastinum — account for 1% to 5% of all germ cell neoplasms

- pelvis, particularly sacrococcygeal teratoma

- ovary

- testis

In females, germ cell tumors account for 30% of ovarian tumors, but only 1 to 3% of ovarian cancers in North America. In younger women germ cell tumors are more common, thus in patients under the age of 21, 60% of ovarian tumors are of the germ cell type, and up to one-third are malignant. In males, germ cell tumors of the testis occur typically after puberty and are malignant (testicular cancer). In neonates, infants, and children younger than 4 years, the majority of germ cell tumors are sacrococcygeal teratomas.

Males with Klinefelter syndrome have a 50 times greater risk of germ cell tumors (GSTs). In these persons, GSTs usually contain nonseminomatous elements, present at an earlier age, and seldom are gonadal in location.

The average age of diagnosis is between 15 and 35 years. This is about 5 to 10 years older than men with other germ cell tumors of the testes. In most cases, they produce masses that are readily felt on testicular self-examination; however, in up to 11 percent of cases, there may be no mass able to be felt, or there may be testicular atrophy. Testicular pain is reported in up to one fifth of cases. Low back pain may occur after metastasis to the retroperitoneum.

Some cases of seminoma can present as a primary tumour outside the testis, most commonly in the mediastinum. In the ovary, the tumor is called a dysgerminoma, and in non-gonadal sites, particularly the central nervous system, it is called a germinoma.

Mixed germ cell tumors occur in many forms. Among these, a common form is teratoma with endodermal sinus tumor.

Teratocarcinoma refers to a germ cell tumor that is a mixture of teratoma with embryonal carcinoma, or with choriocarcinoma, or with both. This kind of mixed germ cell tumor may be known simply as a teratoma with elements of embryonal carcinoma or choriocarcinoma, or simply by ignoring the teratoma component and referring only to its malignant component: embryonal carcinoma and/or choriocarcinoma. They can present in the anterior mediastinum.

Sex cord–gonadal stromal tumour (or sex cord–stromal tumour) is a group of tumors derived from the stromal component of the ovary and testis, which comprises the granulosa, thecal cells and fibrocytes. In contrast, the epithelial cells originate from the outer epithelial lining surrounding the gonad while the germ cell tumors arise from the precursor cells of the gametes, hence the name germ cell. In humans, this group accounts for 8% of ovarian cancers and under 5% of testicular cancers. Their diagnosis is histological: only a biopsy of the tumour can make an exact diagnosis. They are often suspected of being malignant prior to operation, being solid ovarian tumours that tend to occur most commonly in post menopausal women.

This group of tumours is significantly less common than testicular germ cell tumours in men, and slightly less common than ovarian germ cell tumours in women (see Ovarian cancer).

In the ovary, embryonal carcinoma is quite rare, amounting to approximately three percent of ovarian germ cell tumours. The median age at diagnosis is 15 years. Symptoms and signs are varied, and may include sexual precocity and abnormal (increased, reduced or absent) uterine bleeding.

There may be elevations in serum human chorionic gonadotropin (hCG) and alpha fetoprotein (AFP) levels but it would be in association with other tumors, (e.g. yolk sac tumor) because they themselves do not produce the serum markers. At surgery, there is extension of the tumour beyond the ovary in forty percent of cases. They are generally large, unilateral tumours, with a median diameter of 17 centimetres. Long-term survival has improved following the advent of chemotherapy. The gross and histologic features of this tumour are similar to that seen in the testis.

In the testis pure embryonal carcinoma is also uncommon, and accounts for approximately ten percent of testicular germ cell tumours. However, it is present as a component of almost ninety percent of mixed nonseminomatous germ cell tumours. The average age at diagnosis is 31 years, and typically presents as a testicular lump which may be painful. One fifth to two thirds of patients with tumours composed predominantly of embryonal carcinoma have metastases at diagnosis.

Seminoma (also known as "pure seminoma" or "classical seminoma") is a germ cell tumor of the testicle or, more rarely, the mediastinum or other extra-gonadal locations. It is a malignant neoplasm and is one of the most treatable and curable cancers, with a survival rate above 95% if discovered in early stages.

Testicular seminoma originates in the germinal epithelium of the seminiferous tubules. About half of germ cell tumors of the testicles are seminomas. Treatment usually requires removal of one testicle. However, fertility usually isn't affected. All other sexual functions will remain intact.

Due to excess testosterone secreted by the tumour, one-third of female patients present with a recent history of progressive masculinization. Masculinization is preceded by anovulation, oligomenorrhoea, amenorrhoea and defeminization. Additional signs include acne and hirsutism, voice deepening, clitoromegaly, temporal hair recession, and an increase in musculature. Serum testosterone level is high.

These tumours are of the following types, characterized by their abnormal production of otherwise apparently normal cells or tissues.

Although each of the cell and tissue types normally occurs in just one sex (male or female), within a tumour they can occur in the opposite sex. Consequently, depending on the specific histology produced, these tumours can cause virilization in women and feminization in men.

The tumour is subdivided into many different subtypes. The most typical is composed of tubules lined by Sertoli cells and interstitial clusters of Leydig cells.

A malignant mixed Müllerian tumor, also known as malignant mixed mesodermal tumor, MMMT and carcinosarcoma, is a malignant neoplasm found in the uterus, the ovaries, the fallopian tubes and other parts of the body that contains both carcinomatous (epithelial tissue) and sarcomatous (connective tissue) components. It is divided into two types, homologous (in which the sarcomatous component is made of tissues found in the uterus such as endometrial, fibrous and/or smooth muscle tissues) and a heterologous type (made up of tissues not found in the uterus, such as cartilage, skeletal muscle and/or bone). MMMT account for between two and five percent of all tumors derived from the body of the uterus, and are found predominantly in postmenopausal women with an average age of 66 years. Risk factors are similar to those of adenocarcinomas and include obesity, exogenous estrogen therapies, and nulliparity. Less well-understood but potential risk factors include tamoxifen therapy and pelvic irradiation.

Spermatocytic seminoma is a rare tumour, making up only one to two percent of all testicular germ cell tumours. Men presenting with this tumour are generally 50 to 60 years old, and its occurrence is rare in men under 30 years old. Most present with slow, painless testicular enlargement, which may involve both testes.

There is debate over the naming of MMMT; the term carcinosarcoma was formerly used to describe lesions with homologous tumors, and "malignant mixed Müllerian tumor" or "mixed mesodermal tumor" was used to describe heterologous tumors. While "carcinosarcoma" now considered standard, "malignant mixed Müllerian tumor" has a lengthy history within gynecological literature and is expected to continue to be used. The naming issue to a certain extent reflects histological characteristics and development of the tumors, in which the different types of tissues are believed to either develop separately and join into a single mass (the "collision" theory), that an adenocarcinoma stimulates the stroma to create a tumor (the "composition" theory), or that the tumor is the result of a stem cell that differentiates into different cell types (the "combination" theory). "Collision" tumors are normally easily recognized and not considered true MMMTs; the "combination" theory is most widely held, and is due to evidence that the tumors develop from a single line of cells, developing in a fashion similar to the fundus of the uterus from the Müllerian duct - first from a stem cell into a population of cells, that then differentiates into epithelial and stromal components.

There is evidence that some tumors are better explained by the composition theory, due to the aggressive nature of the epithelial cells involved which tend to metastasize much more readily than the sarcomal component. The behavior of MMMT overall is more related to the type and grade of the epithelium than the sarcoma, which suggests the sarcomal portion is an atypical "bystander" than primary driver of the tumor. Despite this, when purely endometrial tumors are compared to MMMTs, the MMMT tumor tends to have a worse prognosis.

Spermatocytic seminoma is a neoplasm of the testis ("i.e." a tumour of the testis), and classified as a germ cell tumour.

The name of the tumour comes from the similarity (under the microscope) between the small cells of the tumour and secondary spermatocytes.

Benign tumors of the ovary include ovarian cysts, such as borderline tumor cysts.

They are exceptionally associated with hypercalcemia. On gross examination, dysgerminomas present with a smooth, bosselated (knobby) external surface, and is soft, fleshy and either cream-coloured, gray, pink or tan when cut. Microscopic examination typically reveals uniform cells that resemble primordial germ cells. Typically, the stroma contains lymphocytes and about 20% of patients have sarcoid-like granulomas.

Metastases are most often present in the lymph nodes.

Ovarian cancer is classified according to the histology of the tumor, obtained in a pathology report. Histology dictates many aspects of clinical treatment, management, and prognosis.

- Surface epithelial-stromal tumours, also known as ovarian epithelial tumors, are the most common type of ovarian cancer. It includes serous tumour, endometrioid tumor, and mucinous tumour. They can be benign (cystadenoma) or malignant (cystadenocarcinoma). Less common tumors are malignant Brenner tumor and transitional cell carcinoma of the ovary.

- Sex cord-stromal tumor, including estrogen-producing granulosa cell tumor and virilizing Sertoli-Leydig cell tumor or arrhenoblastoma, accounts for 8% of ovarian cancers.

- Germ cell tumor accounts for approximately 30% of ovarian tumors but only 5% of ovarian cancers, because most germ cell tumors are teratomas and most teratomas are benign. Germ cell tumors tend to occur in young women (20's-30's) and girls. Whilst overall the prognosis of germ cell tumors tend to be favourable, it can vary substantially with specific histology: for instance, the prognosis of the most common germ cell tumor (dysgerminomas) tends to be good, whilst the second most common (endodermal sinus tumor) tends to have a poor prognosis. In addition, the cancer markers used vary with tumor type: choriocarcinomas are monitored with beta-HCG; dysgerminomas with LDH; and endodermal sinus tumors with alpha-fetoprotein.

- Mixed tumors, containing elements of more than one of the above classes of tumor histology.

Epithelial-stromal tumors are classified on the basis of the epithelial cell type, the relative amounts of epithelium and stroma, the presence of processes, and the location of the epithelial elements. Microscopic pathological features determine whether a surface epithelial-stromal tumor is benign, borderline, or malignant (evidence of malignancy and stromal invasion). Borderline tumors are of uncertain malignant potential.

This group consists of serous, mucinous, endometrioid, clear cell, and brenner (transitional cell) tumors, though there are a few mixed, undifferentiated and unclassified types.

Unlike benign germ cell tumors of the mediastinum, malignant mediastinal tumors are usually symptomatic at the time of diagnosis. Most mediastinal malignant tumors are large and cause symptoms by compressing or invading adjacent structures, including the lungs, pleura, pericardium, and chest wall.

Seminomas grow relatively slowly and can become very large before causing symptoms. Tumors 20 to 30 cm in diameter can exist with minimal symptomatology.

Choriocarcinoma is a malignant, trophoblastic cancer, usually of the placenta. It is characterized by "early hematogenous spread" to the lungs. It belongs to the malignant end of the spectrum in gestational trophoblastic disease (GTD). It is also classified as a germ cell tumor and may arise in the testis or ovary.

A dysgerminoma is a type of germ cell tumor; it usually is malignant and usually occurs in the ovary.

A tumor of the identical histology but not occurring in the ovary may be described by an alternate name: seminoma in the testis or germinoma in the central nervous system or other parts of the body.

Dysgerminoma accounts for less than 1% of ovarian tumors overall. Dysgerminoma usually occurs in adolescence and early adult life; about 5% occur in pre-pubertal children. Dysgerminoma is extremely rare after age 50. Dysgerminoma occurs in both ovaries in 10% of patients and, in a further 10%, there is microscopic tumor in the other ovary.

Abnormal gonads (due to gonadal dysgenesis and androgen insensitivity syndrome) have a high risk of developing a dysgerminoma. Most dysgerminomas are associated with elevated serum lactic dehydrogenase (LDH), which is sometimes used as a tumor marker.

Early signs and symptoms of ovarian cancer may be absent or subtle. In most cases, symptoms exist for several months before being recognized and diagnosed. Symptoms can be misdiagnosed as irritable bowel syndrome. The early stages of ovarian cancer tend to be painless. Symptoms can vary based on the subtype. Low malignant potential (LMP) tumors, also known as borderline tumors, do not cause an increase in CA125 levels and are not identifiable with an ultrasound. The typical symptoms of an LMP tumor can include abdominal distension or pelvic pain. Particularly large masses tend to be benign or borderline.

The most typical symptoms of ovarian cancer include bloating, abdominal or pelvic pain or discomfort, back pain, irregular menstruation or postmenopausal vaginal bleeding, pain or bleeding after or during sexual intercourse, loss of appetite, fatigue, diarrhea, indigestion, heartburn, constipation, nausea, feeling full, and possibly urinary symptoms (including frequent urination and urgent urination).

Mediastinal germ cell tumors are tumors that derive from germ cell rest remnants in the mediastinum. They most commonly occur in the gonad but occasionally elsewhere.