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.

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.

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.

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.

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.

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.

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.

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.

Spermatocytic seminoma is not considered a subtype of seminoma and, unlike seminoma and most other germ cell tumours, it does not arise from "intratubular germ cell neoplasia". It has not been described as arising in locations outside the testis, and does not occur in association with other germ cell tumours.

The new WHO classification, due to be published in 2016, will rename the condition spermatocytic tumour to avoid confusion with classical seminoma as the biology and treatment are different.

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).

Estrogens are produced by "functioning" tumours, and the clinical presentation depends on the patient's age and sex.

- Female

- If the patient is postmenopausal, she usually presents with abnormal uterine bleeding, and in some cases hemoperitoneum.

- If the patient is of reproductive age, she would present with menometrorrhagia. However, in some cases she may stop ovulating altogether.

- If the patient has not undergone puberty, early onset of puberty may be seen.

- these tumors tend to have late recurrencies ( even after 30 years )

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.

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.

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.

Granulosa cell tumours (or granulosa-theca cell tumours or folliculoma) are tumours that arise from granulosa cells. These tumours are part of the sex cord-gonadal stromal tumour or non-epithelial group of tumours. Although granulosa cells normally occur only in the ovary, granulosa cell tumours occur in both ovaries and testicles (see Ovarian cancer and Testicular cancer). These tumours should be considered malignant and treated in the same way as other malignant tumours of ovary. The ovarian disease has two forms, juvenile and adult, both characterized by indolent growth, and therefore has high recovery rates.

The staging system for these tumours is the same as for epithelial tumours and most present as stage I. The peak age at which they occur is 50–55 years, but they may occur at any age.

Juvenile granulosa cell tumour is a similar but distinct rare tumour. It too occurs in both the ovary and testis. In the testis it is extremely rare, and has not been reported to be malignant. Although this tumour usually occurs in children (hence its name), it has been reported in adults.

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.

Dysgerminoma is the most common type of malignant germ cell ovarian cancer. 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.

Seminoma is the second most common testicular cancer; the most common is mixed, which may contain seminoma.

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.

Metastases are most often present in the lymph nodes.

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.

The term "germinoma" most often refers to a tumor in the brain that has a histology identical to two other tumors: dysgerminoma in the ovary and seminoma in the testis. Since 1994, MeSH has defined germinoma as "a malignant neoplasm of the germinal tissue of the gonads; mediastinum; or pineal region" and within its scope included both dysgerminoma and seminoma. Collectively, these are the seminomatous or germinomatous tumors.

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.

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

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.

Gonadoblastoma is most often associated with an abnormal chromosomal karyotype, gonadal dysgenesis, or the presence of a Y chromosome in over 90% of cases. Gonadoblastoma has been found in association with androgen insensitivity syndrome, mixed gonadal dysgenesis and Turner syndrome, especially in the presence of Y chromosome-bearing cells.

Gonadoblastomas can contain elements of both germ cells and gonadal stroma.

Formerly, gonadoblastoma was sometimes regarded as a subset of dysgerminoma. In modern literature, it is sometimes considered to progress to dysgerminoma.