The diagnosis of this syndrome can be made on clinical examination and perinatal autopsy.

Koenig and Spranger (1986) noted that eye lesions are apparently nonobligatory components of the syndrome. The diagnosis of Fraser syndrome should be entertained in patients with a combination of acrofacial and urogenital malformations with or without cryptophthalmos. Thomas et al. (1986) also emphasized the occurrence of the cryptophthalmos syndrome without cryptophthalmos and proposed diagnostic criteria for Fraser syndrome. Major criteria consisted of cryptophthalmos, syndactyly, abnormal genitalia, and positive family history. Minor criteria were congenital malformation of the nose, ears, or larynx, cleft lip and/or palate, skeletal defects, umbilical hernia, renal agenesis, and mental retardation. Diagnosis was based on the presence of at least 2 major and 1 minor criteria, or 1 major and 4 minor criteria.

Boyd et al. (1988) suggested that prenatal diagnosis by ultrasound examination of eyes, digits, and kidneys should detect the severe form of the syndrome. Serville et al. (1989) demonstrated the feasibility of ultrasonographic diagnosis of the Fraser syndrome at 18 weeks' gestation. They suggested that the diagnosis could be made if 2 of the following signs are present: obstructive uropathy, microphthalmia, syndactyly, and oligohydramnios. Schauer et al. (1990) made the diagnosis at 18.5 weeks' gestation on the basis of sonography. Both the female fetus and the phenotypically normal father had a chromosome anomaly: inv(9)(p11q21). An earlier born infant had Fraser syndrome and the same chromosome 9 inversion.

Van Haelst et al. (2007) provided a revision of the diagnostic criteria for Fraser syndrome according to Thomas et al. (1986) through the addition of airway tract and urinary tract anomalies to the major criteria and removal of mental retardation and clefting as criteria. Major criteria included syndactyly, cryptophthalmos spectrum, urinary tract abnormalities, ambiguous genitalia, laryngeal and tracheal anomalies, and positive family history. Minor criteria included anorectal defects, dysplastic ears, skull ossification defects, umbilical abnormalities, and nasal anomalies. Cleft lip and/or palate, cardiac malformations, musculoskeletal anomalies, and mental retardation were considered uncommon. Van Haelst et al. (2007) suggested that the diagnosis of Fraser syndrome can be made if either 3 major criteria, or 2 major and 2 minor criteria, or 1 major and 3 minor criteria are present in a patient.

Townes–Brocks syndrome (TBS) is a rare genetic disease that has been described in approximately 200 cases in the published literature. It affects both males and females equally. The condition was first identified in 1972. by Philip L. Townes, MD, PhD, who was at the time a human geneticists and Professor of Pediatrics, and Eric Brocks, MD, who was at the time a medical student, both at the University of Rochester.

TBS is an autosomal dominant involving the a mutation of the gene SALL1, which encodes a transcriptional repressor which interacts with TRF1/PIN2 and localizes to pericentromeric heterochromatin. The clinical features of TBS overlap with VATER and VACTERL associations, oculo-auriculo-vertebral (OAV) spectrum, branchio-oto-renal (BOR) syndrome, and Fanconi anemia and other 'anus-hand-ear' syndromes.

Although some symptoms can be life-threatening, many people diagnosed with Townes-Brocks Syndrome live a normal lifespan.

The incidence of Fraser syndrome is 0.043 per 10,000 live born infants and 1.1 in 10,000 stillbirths, making it a rare syndrome.

Patients with abnormal cardiac and kidney function may be more at risk for hemolytic uremic syndrome

Fertility options for girls and women with Rokitansky-Mayer-Küster-Hauser syndrome has a bit more information. Girls and women who are born without a complete vagina, but still have a regular sized uterus more than likely will be able to become pregnant and have a baby. However, if the female is born with a tiny uterus, or without a uterus, they will not be able to have a baby. As the ovaries may be normal in this case, the egg may be fertilized with a donor's or partner's sperm. In this case, surrogacy, would be an option where there will be a gestational carrier to carry the pregnancy for the couple. Adoption may also be an option for females with Rokitansky-Mayer-Küster-Hauser syndrome. Another possibility could be uterine transplants, however this a new and developing form of treatment. Fertility options are being researched daily, so there can always be a new method available.

Any pain associated with Rokitansky-Mayer-Küster-Hauser syndrome comes from menstruation related cramping and can be treated with several ways. Individuals with this syndrome may be born with a uterine remnant (tiny uterus), which can fill with become filled with blood in the pelvic cavity causing pain. A medical professional can assess the severity of having a uterine remnant within each patient to determine if removal of the uterus is necessary.

The prognosis for vaginal atresia is one that is complicated. There are variations in patients' anatomic findings as well as an absence in consistent surgical techniques which makes it difficult to give a prognosis for this condition. Along with other conditions that give rise to an abnormal perineum (i.e. ambiguous genitalia and other various abnormalities that range from cloaca to urogenital sinus), individuals with vaginal atresia often report reconstruction as an outcome of treatment. Due to this, it is difficult to compare outcomes between individuals with vaginal atresia.

Diphallia, penile duplication (PD), diphallic terata, or diphallasparatus, is a rare developmental abnormality in which a male is born with two penises. The first reported case was by Johannes Jacob Wecker in 1609. Its occurrence is 1 in 5.5 million boys in the United States.

When diphallia is present, it is usually accompanied by renal, vertebral, hindgut, anorectal or other congenital anomalies. There is also a higher risk of spina bifida. Infants born with PD and its related conditions have a higher death rate from various infections associated with their more complex renal or colorectal systems.

It is thought diphallia occurs in the fetus between the 23rd and 25th days of gestation when an injury, chemical stress, or malfunctioning homeobox genes hamper proper function of the caudal cell mass of the fetal mesoderm as the urogenital sinus separates from the genital tubercle and rectum to form the penis.

The incidence of VACTERL association is estimated to be approximately 1 in 10,000 to 1 in 40,000 live-born infants. It is seen more frequently in infants born to diabetic mothers. While most cases are sporadic, there are clearly families who present with multiple involved members.

This condition may be visible, after about 26 weeks, on an ultrasound. On antenatal USG, the finding of an absent or small stomach in the setting of polyhydramnios was considered a potential symptom of esophageal atresia. However, these findings have a low positive predictive value. The upper neck pouch sign is another sign that helps in the antenatal diagnosis of esophageal atresia and it may be detected soon after birth as the affected infant will be unable to swallow its own saliva. Also, the newborn can present with gastric distention, cough, apnea, tachypnea, and cyanosis. In many types of esophageal atresia, a feeding tube will not pass through the esophagus.

This condition takes several different forms, often involving one or more fistulas connecting the trachea to the esophagus (tracheoesophageal fistula).

When an infant is born with an anorectal malformation, it is usually detected quickly as it is a very obvious defect. Doctors will then determine the type of birth defect the child was born with and whether or not there are any associated malformations. It is important to determine the presence of any associated defects during the newborn period in order to treat them early and avoid further sequelae. There are two main categories of anorectal malformations: those that require a protective colostomy and those that do not. The decision to open a colostomy is usually taken within the first 24 hours of birth.

Sonography can be used to determine the type of imperforate anus.

With a high lesion, many children have problems controlling bowel function and most also become constipated. With a low lesion, children generally have good bowel control, but they may still become constipated.

For children who have a poor outcome for continence and constipation from the initial surgery, further surgery to better establish the angle between the anus and the rectum may improve continence and, for those with a large rectum, surgery to remove that dilated segment may significantly improve the bowel control for the patient. An antegrade enema mechanism can be established by joining the appendix to the skin (Malone stoma); however, establishing more normal anatomy is the priority.

After removal, the testicle is fixed with Bouin's solution because it better conserves some morphological details such as nuclear conformation. Then the testicular tumor is staged by a pathologist according to the TNM Classification of Malignant Tumors as published in the AJCC Cancer Staging Manual. Testicular cancer is categorized as being in one of three stages (which have subclassifications). The size of the tumor in the testis is irrelevant to staging. In broad terms, testicular cancer is staged as follows:

- Stage I: the cancer remains localized to the testis.

- Stage II: the cancer involves the testis and metastasis to retroperitoneal and/or paraaortic lymph nodes (lymph nodes below the diaphragm).

- Stage III: the cancer involves the testis and metastasis beyond the retroperitoneal and paraaortic lymph nodes. Stage 3 is further subdivided into non-bulky stage 3 and bulky stage 3.

Further information on the detailed staging system is available on the website of the American Cancer Society.

Treatment for fistula varies depending on the cause and extent of the fistula, but often involves surgical intervention combined with antibiotic therapy.

Typically the first step in treating a fistula is an examination by a doctor to determine the extent and "path" that the fistula takes through the tissue.

In some cases the fistula is temporarily covered, for example a fistula caused by cleft palate is often treated with a palatal obturator to delay the need for surgery to a more appropriate age.

Surgery is often required to assure adequate drainage of the fistula (so that pus may escape without forming an abscess). Various surgical procedures are commonly used, most commonly fistulotomy, placement of a seton (a cord that is passed through the path of the fistula to keep it open for draining), or an endorectal flap procedure (where healthy tissue is pulled over the internal side of the fistula to keep feces or other material from reinfecting the channel). Treatment involves filling the fistula with fibrin glue; also plugging it with plugs made of porcine small intestine submucosa have also been explored in recent years, with variable success. Surgery for anorectal fistulae is not without side effects, including recurrence, reinfection, and incontinence. High rate of recurrence and more chances of complications like incontinence are always there in fistula surgeries (Anal Fistula).

It is important to note that surgical treatment of a fistula without diagnosis or management of the underlying condition, if any, is not recommended. For example, surgical treatment of fistulae in Crohn's disease can be effective, but if the Crohn's disease itself is not treated, the rate of recurrence of fistula is very high (well above 50%).

The main way testicular cancer is diagnosed is via a lump or mass inside a testis. More generally, if a young adult or adolescent has a single enlarged testicle, which may or may not be painful, this should give doctors reason to suspect testicular cancer.

Other conditions may also have symptoms similar to testicular cancer:

- Epididymitis or epididymoorchitis

- Hematocele

- Varicocele

- Orchitis

- Prostate infections or inflammations (prostatitis), bladder infections or inflammations (cystitis), or kidney (renal) infections (nephritis) or inflammations which have spread to and caused swelling in the vessels of the testicles or scrotum

- Testicular torsion or a hernia

- Infection, inflammation, retro-peritonitis, or other conditions of the lymph nodes or vessels near the scrotum, testicles, pubis, anorectal area, and groin

- Benign tumors or lesions of the testicles

- Metastasis to the testicles from another, primary tumor site(s)

The nature of any palpated lump in the scrotum is often evaluated by scrotal ultrasound, which can determine exact location, size, and some characteristics of the lump, such as cystic vs solid, uniform vs heterogeneous, sharply circumscribed or poorly defined. The extent of the disease is evaluated by CT scans, which are used to locate metastases.

The differential diagnosis of testicular cancer requires examining the histology of tissue obtained from an inguinal orchiectomy - that is, surgical excision of the entire testis along with attached structures (epididymis and spermatic cord). A biopsy should not be performed, as it raises the risk of spreading cancer cells into the scrotum.

Inguinal orchiectomy is the preferred method because it lowers the risk of cancer cells escaping. This is because the lymphatic system of the scrotum, through which white blood cells (and, potentially, cancer cells) flow in and out, links to the lower extremities, while that of the testicle links to the back of the abdominal cavity (the retroperitoneum). A transscrotal biopsy or orchiectomy will potentially leave cancer cells in the scrotum and create two routes for cancer cells to spread, while in an inguinal orchiectomy only the retroperitoneal route exists.

Blood tests are also used to identify and measure tumor markers (usually proteins present in the bloodstream) that are specific to testicular cancer. Alpha-fetoprotein, human chorionic gonadotropin (the "pregnancy hormone"), and LDH-1 are the typical tumor markers used to spot testicular germ cell tumors.

A pregnancy test may be used to detect high levels of chorionic gonadotropin; however, the first sign of testicular cancer is usually a painless lump. Note that only about 25% of seminomas have elevated chorionic gonadotropin, so a pregnancy test is not very sensitive for making out testicular cancer.

In people with renal failure, requiring dialysis, a cimino fistula is often deliberately created in the arm by means of a short day surgery in order to permit easier withdrawal of blood for hemodialysis.

As a radical treatment for portal hypertension, surgical creation of a portacaval fistula produces an anastomosis between the hepatic portal vein and the inferior vena cava across the omental foramen (of Winslow). This spares the portal venous system from high pressure which can cause esophageal varices, caput medusae, and hemorrhoids.