Standard treatment would include surgical exploration via laparotomy. Laparoscopy may be an option if the surgeon is particularly skilled in removing ovarian neoplasms via laparoscopy intact. If the diagnosis of gonadoblastoma is certain, a bilateral salpingo-oophorectomy (BSO) should be performed to remove both the primary tumor and the dysgenic contralateral ovary. If uninvolved, the uterus should be left intact. Modern reproductive endocrinology technology allows patients post BSO to achieve pregnancy via in-vitro fertilization (IVF) with a donor egg.

A gonadal tissue neoplasm is a tumor having any histology characteristic of cells or tissues giving rise to the gonads. These tissues arise from the sex cord and stromal cells. The tumor may be derived from these tissues, or produce them.

Although the tumor is composed of gonadal tissue, it is not necessarily located in an ovary or testicle.

A gonadal tissue neoplasm should not be confused with a urogenital neoplasm, though the two topics are often studied together. The embryology of the gonads is only indirectly related to the embryology of the external genitals and urinary system.

A urogenital neoplasm is a tumor of the urogenital system.

Types include:

- Cancer of the breast and female genital organs: (Breast cancer, Vulvar cancer, Vaginal cancer, Cervical cancer, Uterine cancer, Endometrial cancer, Ovarian cancer)

- Cancer of the male genital organs (Carcinoma of the penis, Prostate cancer, Testicular cancer)

- Cancer of the urinary organs (Renal cell carcinoma, Bladder cancer)

The average age at time of EIN diagnosis is approximately 52 years, compared to approximately 61 years for carcinoma. The timeframe and likelihood of EIN progression to cancer, however, is not constant amongst all women. Some cases of EIN are first detected as residual premalignant disease in women who already have carcinoma, whereas other EIN lesions disappear entirely and never lead to cancer. For this reason, treatment benefits and risks must be individualized for each patient under the guidance of an experienced physician.

Risk factors for development of EIN and the endometrioid type of endometrial carcinoma include exposure to estrogens without opposing progestins, obesity, diabetes, and rare hereditary conditions such as hereditary nonpolyposis colorectal cancer. Protective factors include use of combined oral contraceptive pills (low dose estrogen and progestin), and prior use of a contraceptive intrauterine device.

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.

Treatment may include the following:

- Surgery with or without radiation

- Radiotherapy

Fast neutron therapy has been used successfully to treat salivary gland tumors, and has shown to be significantly more effective than photons in studies treating unresectable salivary gland tumors.

- Chemotherapy

Acrospiroma (also known as hidradenoma) is a cutaneous condition, primarily occurring in adult women, that is a form of benign adnexal neoplasm closely related to poroma.

Wide, radical, complete surgical excision is the treatment of choice, with free surgical margins to achieve the best outcome and lowest chance of recurrence. Radiation is only used for palliation. In general, there is a good prognosis, although approximately 50% of patients die from disease within 3–10 years of presentation.

Women with benign germ cell tumors such as mature teratomas (dermoid cysts) are cured by ovarian cystectomy or oophorectomy. In general, all patients with malignant germ cell tumors will have the same staging surgery that is done for epithelial ovarian cancer. If the patient is in her reproductive years, an alternative is unilateral salpingoophorectomy, while the uterus, the ovary, and the fallopian tube on the opposite side can be left behind. This isn't an option when the cancer is in both ovaries. If the patient has finished having children, the surgery involves complete staging including salpingoophorectomy on both sides as well as hysterectomy.

Most patients with germ cell cancer will need to be treated with combination chemotherapy for at least 3 cycles. The chemotherapy regimen most commonly used in germ cell tumors is called PEB (or BEP), and consists of bleomycin, etoposide, a platinum-based antineoplastic (cisplatin).

The 1997 International Germ Cell Consensus Classification is a tool for estimating the risk of relapse after treatment of malignant germ cell tumor.

A small study of ovarian tumors in girls reports a correlation between cystic and benign tumors and, conversely, solid and malignant tumors. Because the cystic extent of a tumor can be estimated by ultrasound, MRI, or CT scan before surgery, this permits selection of the most appropriate surgical plan to minimize risk of spillage of a malignant tumor.

Access to appropriate treatment has a large effect on outcome. A 1993 study of outcomes in Scotland found that for 454 men with non-seminomatous (non-germinomatous) germ cell tumors diagnosed between 1975 and 1989, 5-year survival increased over time and with earlier diagnosis. Adjusting for these and other factors, survival was 60% higher for men treated in a cancer unit that treated the majority of these men, even though the unit treated more men with the worst prognosis.

Choriocarcinoma of the testicles has the worst prognosis of all germ cell cancers

These lesions rarely require surgery unless they are symptomatic or the diagnosis is in question. Since these lesions do not have malignant potential, long-term observation is unnecessary. Surgery can include the removal of the head of the pancreas (a pancreaticoduodenectomy), removal of the body and tail of the pancreas (a distal pancreatectomy), or rarely removal of the entire pancreas (a total pancreatectomy). In selected cases the surgery can be performed using minimally invasive techniques such as laparoscopy.

Complete surgical excision is the treatment of choice, associated with an excellent long term clinical outcome.

Endometrial intraepithelial neoplasia (EIN) is a premalignant lesion of the uterine lining that predisposes to endometrioid endometrial adenocarcinoma. It is composed of a collection of abnormal endometrial cells, arising from the glands that line the uterus, which have a tendency over time to progress to the most common form of uterine cancer—endometrial adenocarcinoma, endometrioid type.

The treatment of choice for main-duct IPMNs is resection due to approximately 50% chance of malignancy. Side-branch IPMNs are occasionally monitored with regular CT or MRIs, but most are eventually resected, with a 30% rate of malignancy in these resected tumors. Survival 5 years after resection of an IPMN without malignancy is approximately 80%, 85% with malignancy but no lymph node spread and 0% with malignancy spreading to lymph nodes. Surgery can include the removal of the head of the pancreas (a pancreaticoduodenectomy), removal of the body and tail of the pancreas (a distal pancreatectomy), or rarely removal of the entire pancreas (a total pancreatectomy). In selected cases the surgery can be performed using minimally invasive techniques such as laparoscopy or robotic surgery. A study using Surveillance, Epidemiology, and End Result Registry (SEER) data suggested that increased lymph node counts harvested during the surgery were associated with better survival in invasive IPMN patients.

Clear cell ovarian tumors are part of the surface epithelial-stromal tumor group of ovarian cancers, accounting for 6% of these cancers. Clear cell tumors are also associated with the pancreas and salivary glands.

Sebaceous lymphadenoma is a tissue diagnosis, e.g. salivary gland biopsy.

It may be confused with a number of benign and malignant neoplasms, including Warthin tumour, mucoepidermoid carcinoma and sebaceous lymphadenocarcinoma.

Ceruminous adenocarcinoma is a malignant neoplasm derived from ceruminous glands of the external auditory canal. This tumor is rare, with several names used in the past. Synonyms have included cylindroma, ceruminoma, ceruminous adenocarcinoma, not otherwise specified (NOS), ceruminous adenoid cystic carcinoma (ACC), and ceruminous mucoepidermoid carcinoma.

The tumor is rare, affecting adults in the 4th decade most commonly. Patients are usually younger than those who present with a lipoma. There is a slight male predominance. Hibernoma are most commonly identified in the subcutaneous and muscle tissue of the head and neck region (shoulders, neck, scapular), followed by thigh, back, chest, abdomen, and arms. In rare cases hibernoma may arise in bone tissue, however it is an incidental finding.

Papillary eccrine adenoma (also known as "tubular apocrine adenoma") is a cutaneous condition characterized by an uncommon benign sweat gland neoplasm that presents as a dermal nodule located primarily on the extremities of black patients.

Intraductal papillary mucinous neoplasm (IPMN) is a type of tumor that can occur within the cells of the pancreatic duct. IPMN tumors produce mucus, and this mucus can form pancreatic cysts. Although intraductal papillary mucinous neoplasms are benign tumors, they can progress to pancreatic cancer. As such IPMN is viewed as a precancerous condition. Once an intraductal papillary mucinous neoplasm has been found, the management options include close monitoring and pre-emptive surgery.

Chemotherapeutic options include:

- Cyclophosphamide plus methotrexate plus fluorouracil (CMF).

- Cyclophosphamide plus doxorubicin plus fluorouracil (CAF).

- Trastuzumab (monoclonal antibody therapy).

Hormonal options include:

- Orchiectomy.

- Gonadotropin hormone releasing hormone agonist (GNRH agonist) with or without total androgen blockage (anti-androgen).

- Tamoxifen for estrogen receptor–positive patients.

- Progesterone.

- Aromatase inhibitors.

The treatment is simple excision and exclusion of a malignant neoplasm.

Pancreatic serous cystadenoma, also known as serous cystadenoma of the pancreas and serous microcystic adenoma, a benign tumour of pancreas. It is usually found in the head of the pancreas, and may be associated with von Hippel-Lindau syndrome.

In contrast to some of the other cyst-forming tumors of the pancreas (such as the intraductal papillary mucinous neoplasm and the mucinous cystic neoplasm), serous cystic neoplasms are almost always entirely benign. There are some exceptions; rare case reports have described isolated malignant serous cystadenocarcinomas. In addition, serous cystic neoplasms slowly grow, and if they grow large enough they can press on adjacent organs and cause symptoms.

Testicular dysgenesis syndrome is a male reproduction-related condition characterized by the presence of symptoms and disorders such as hypospadias, cryptorchidism, poor semen quality, and testicular cancer.

The concept was first introduced by N.E. Skakkaebaek in a research paper along with the department of Growth and Reproduction in Copenhagen University. The paper suggests the origin and underlying cause of TDS can be detected as early as in fetal life, where environmental and genomic factors could affect the development of the male reproductive system

A problem for people with penile agenesis is the absence of a urinary outlet. Before genital metamorphosis, the urethra runs down the anal wall, to be pulled away by the genital tubercle during male development. Without male development this does not occur. The urethra can be surgically redirected to the rim of the anus immediately after birth to enable urination and avoid consequent internal irritation from urea concentrate. In such cases, the perineum may be left devoid of any genitalia, male or female.

A working penis transplant on to an agenetic patient has never been successful. Only one major penis graft was successfully completed. This occurred in China and the patient shortly rejected it on psychological grounds. However a full female or agenetic to male transplant is not yet facilitated to fulfil full reproductive functions.

On March 18, 2013, it was announced that Andrew Wardle, a British man born without a penis, was going to receive a pioneering surgery to create a penis for him. The surgeons hope to "fold a large flap of skin from his arm — complete with its blood vessels and nerves — into a tube to graft onto his pubic area." If the surgery goes well, the odds of starting a family are very good.