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Genital Birth Defects


Ronald Rabinowitz

, MD, University of Rochester Medical Center;

Jimena Cubillos

, MD, University of Rochester School of Medicine and Dentistry

Last full review/revision Oct 2020| Content last modified Oct 2020

Defects of the genitals can involve the penis, scrotum, or testes (testicles) in boys and the vagina and labia in girls. Sometimes the genitals are ambiguous, that is, not clearly female or male.

  • Genital defects may be caused by abnormal levels of sex hormones during fetal development, chromosome abnormalities, environmental factors, or inherited factors.
  • Sometimes the genitals are not clearly male or female (ambiguous genitals), which is most common in girls with congenital adrenal hyperplasia.
  • To determine the sex of an infant who has ambiguous genitals, a physical examination, imaging tests, and blood tests to analyze chromosomes and measure hormone levels are done.
  • Many genital defects require surgery.
  • Parents have many factors to consider before assigning a gender to a baby born with ambiguous genitals.

(See also Overview of Kidney and Urinary Tract Birth Defects.)

Causes of Genital Birth Defects

Male and female sex organs develop from similar tissue in the embryo. Whether this tissue develops into male or female sex organs depends on a number of things. One factor is the sex chromosomes, which are called X and Y. Normal males have one X and one Y chromosome. Normal females have two X chromosomes. Early in development, a fetus with a Y chromosome begins developing testes, which secrete the male hormone testosterone. Testosterone activates pathways that cause development of the scrotum, penis, and penile urethra (the urine passage through the penis). Without testosterone (as in a normal female fetus), the genitals become the clitoris, labia majora, and separate vaginal and urethral canals. In addition to testosterone, there are other substances made by the developing fetus that help control genital development.

Factors that can interfere with development of the genitals include

  • Sex chromosome abnormalities
  • Abnormal or missing genes (the DNA code of instructions for how the body works)
  • Exposure of the fetus to substances, such as certain drugs and hormones, that interfere with genital development

In many of these factors, the common problem is abnormal levels of sex hormones in the fetus before birth, particularly having too much testosterone (or testosterone-like substances) in girls and too little testosterone in boys.

Sometimes, the disorder that causes genital defects also results in defects of other organs.

Symptoms of Genital Birth Defects

Sometimes genitals appear abnormal but are still apparently male or female. Such defects in boys include abnormalities of the urethral opening (for example, being located on the bottom or, less often, the top of the penis), an abnormally shaped penis (chordee), and an undescended testis. Defects in girls include a hymen that has no opening (imperforate hymen) and a missing or shortened vagina.

Other defects result in genitals that are not clearly male or female. These are called ambiguous genitals. The most common cause of ambiguous genitals is in girls who have congenital adrenal hyperplasia. Congenital adrenal hyperplasia is an inherited problem with the adrenal glands that causes the glands to produce too much testosterone (the adrenal glands naturally produce a small amount of testosterone in healthy girls).

Children who have genital defects may have problems urinating. Later, people may have difficulties engaging in sexual intercourse, impaired fertility, social and psychologic problems, or a combination.

Did You Know...

  • Children may be born with genitals that are not clearly male or female. These are called ambiguous genitals.

Diagnosis of Genital Birth Defects

  • Physical examination
  • Sometimes imaging tests, such as ultrasonography and magnetic resonance imaging
  • Sometimes blood tests to analyze the chromosomes and hormone levels

Doctors do a physical examination of the child's genitals and look for other birth defects.

Often, doctors do ultrasonography or sometimes magnetic resonance imaging (MRI) to identify the presence of testes, ovaries, and a vagina. They may also use a flexible scope (endoscope) to look in the opening of the urethra and/or vagina to detect abnormalities. If the results of these tests are unclear, doctors may do laparoscopy, in which they look inside the abdominal cavity using an endoscope.

Doctors usually do blood tests to see what sex chromosomes the infant has and to measure hormone levels.

Treatment of Genital Birth Defects

  • For genital defects, surgery
  • For ambiguous genitals, sometimes gender assignment surgery and hormones

Most children who have genital defects need surgery to correct the defects. Some minor defects do not need surgery.

Regarding children with ambiguous genitals, children's sex chromosomes (that is, whether they are a genetic female with XX chromosomes or a genetic male with XY chromosomes) are an important factor, but other things also must be considered. For example, the hormones the fetus was exposed to in the uterus can have a significant effect. However, this effect may not be apparent until children are old enough to begin acting like one gender or another or to think of themselves as one gender or another (gender identity). Because children's behavior and gender identity do not always match their genetic gender, it is important not to make the gender assignment too soon. Waiting is not harmful because it is not essential to assign a gender during infancy. A multidisciplinary care team that includes the pediatrician, endocrinologists (specialists in hormone disorders), geneticists, urologists, and possibly psychiatrists can advise parents facing this challenging decision.

When appropriate and indicated, surgery is done and children are given hormones. Children may need to take hormones for the rest of their life.

Female Genital Defects

There are several causes of female genital defects, but most involve abnormal levels of sex hormones in the fetus before birth.

Some genital birth defects in girls include

  • Ambiguous genitals (genitals that are not clearly male or female), which is often caused by congenital adrenal hyperplasia
  • Imperforate hymen
  • Labial adhesions
  • Extra genital organs (duplication abnormalities)
  • Genital organs joined together (fusion abnormalities)

Rarely, the vagina may be missing or shortened.

To diagnose genital birth defects, doctors do a physical examination and tests.

External Female Genital Organs

External Female Genital Organs

Congenital adrenal hyperplasia

Congenital adrenal hyperplasia is the most common cause of ambiguous genitals in girls. Congenital adrenal hyperplasia is an inherited disorder of the adrenal glands (the adrenals are glands located on the top of each kidney that secrete several types of hormones). In this disorder, the glands are missing enzymes that help produce certain life-sustaining hormones, such as cortisol. Instead, the chemical building blocks that the glands use to make the cortisol are turned into male hormones, such as testosterone.

In infant girls, this build-up of testosterone causes them to develop male sexual characteristics (virilization). Infant girls with the most severe form look like boys with what appears to be a normal penis and scrotum. The penis is actually the clitoris, which has been stimulated to grow by testosterone. The scrotum is actually the labia, which have grown together. However, there are no testes (testicles) in the apparent scrotum. The girls also have darkened nipples and genitals.

In infant boys, the extra testosterone does not affect the appearance of their genitals. However, later in childhood, the penis and pubic hair start to develop at too young an age (early puberty).

Both boys and girls develop life-threatening symptoms because their adrenal glands do not make enough of the normal adrenal hormones. Infants can have serious abnormalities of electrolytes (minerals such as sodium and potassium) in the blood and also become very dehydrated.

Infant girls and boys usually need fluids given by vein (intravenously) and corticosteroid drugs to treat dehydration and electrolyte abnormalities caused by the adrenal hormone deficiency.

Girls may need surgery and hormone supplements.

Imperforate hymen

The hymen is the thin membrane at the opening of the vagina. Usually, the hymen covers only part of the opening. However, some girls are born with a hymen that completely closes the vaginal opening (called an imperforate hymen). Because the vaginal opening is closed, vaginal secretions cannot go out. Sometimes the problem is not detected and repaired when girls are young so when girls begin having menstrual periods, the blood cannot go out. In such cases, girls may have pain because menstrual blood is trapped in their vagina.

Girls who have an imperforate hymen have a minor surgical procedure to open the hymen.

Labial adhesions

The labia are the fleshy lips at the opening of the vagina. Labial adhesions are when the lips of the vagina stick together. These adhesions typically occur in childhood, usually when girls are around 2 years of age, but may develop earlier or later. Labial adhesions usually do not cause symptoms and frequently go away spontaneously. When they do cause symptoms, it is usually because some urine collects in the vagina, which may lead to irritation, infections, or dribbling.

Girls who have labial adhesions that cause symptoms are given a cream that contains estrogen. Alternatively, doctors may split open the adhesions either in the office or in the operating room. Labial adhesions commonly return. To help prevent their return, girls apply another cream several times a day to protect the area from irritation that can cause the adhesions to return. Adhesions that do not cause symptoms should still be split open before puberty so that menstrual blood can properly drain.

Extra genital organs (duplication abnormalities)

Rarely, girls are born with extra (duplicated) genital organs. That is, they may have two vaginas, two cervixes, or a double uterus instead of one. Sometimes, these abnormalities are noticed at birth, but, often, they are not discovered until later in life when there are urinary, menstrual, or pregnancy problems.

Some duplication abnormalities do not require treatment, but others need to be corrected with surgery.

Genital organs joined together (fusion abnormalities)

Rarely, girls' genital organs are joined together (fused) at birth. That is, their rectum, vagina, and urethra may join together as one structure. Sometimes, these abnormalities are noticed at birth, but, often, they are not discovered until later in life when there are urinary, menstrual, or pregnancy problems.

Fusion abnormalities may not require treatment, but others need to be corrected with surgery.

Internal Female Genital Organs

Internal Female Genital Organs

Male Genital Defects

There are several causes of male genital defects, but most involve abnormal levels of sex hormones in the fetus before birth.

Defects of the penis may interfere with a boy's ability to direct the stream of urine while standing. For older males, the defects may interfere with sperm delivery, which may impair fertility, and the ability to have sexual intercourse. These defects can also cause problems with self-esteem because of their appearance.

Common genital birth defects in boys include

  • Urethral opening in the wrong place (hypospadias and epispadias)
  • Unusually small penis (microphallus)
  • Abnormal curvature of the penis (chordee)
  • A foreskin that is too tight (phimosis)
  • Undescended testes

Some boys are born with genitals that are not clearly male or female (called ambiguous genitals). A common cause of ambiguous genitals in boys is testosterone deficiency during early pregnancy (see also Male Hypogonadism in Children).

To diagnose genital birth defects, doctors do a physical examination and tests.

Male Reproductive Organs

Male Reproductive Organs


In hypospadias, the opening of the urethra (the tube that drains urine from the bladder out of the body) is on the underside of the penis:

  • Mild hypospadias: The opening is located just below the normal position on the tip of the penis.
  • Moderate hypospadias: The opening is located somewhere on the shaft of the penis.
  • Severe hypospadias: The opening may be located in the scrotum or between the scrotum and the anus.

Because urine may spray downward, boys who have severe hypospadias may need to sit down to urinate. Boys who have hypospadias often have another defect called chordee (a downward bend of the penis) and an incompletely developed foreskin, in which the foreskin is located on the top of the penis and does not encircle the underside (called a hooded foreskin because it looks like a hood on the penis). The more severe the hypospadias, the more severe the chordee and foreskin abnormalities.

Before removing the foreskin (circumcising) in a newborn with hypospadias, parents should consult a urologist (a doctor who specialize in the diagnosis and treatment of disorders of the urinary tract and male reproductive system). Sometimes doctors need the foreskin tissue when they do surgery to correct hypospadias.

Mild hypospadias may not need treatment. Other children usually have surgery to correct the defect at about 6 months of age. Often the surgery can be done on an outpatient basis (the child does not have to stay in the hospital overnight).

Examples of Hypospadias


In epispadias, the opening of the urethra is located on the top side of the penis instead of at the tip. Children who have epispadias may leak urine (urinary incontinence). Boys who have the most severe form of epispadias often also have another disorder called bladder exstrophy. In bladder exstrophy, the bladder does not completely close and opens out onto the surface of the abdomen, allowing urine to drip through the open bladder rather than the urethra.

Surgery is done to correct epispadias.

Unusually small penis (micropenis)

Some boys have an unusually small penis. This defect is called micropenis or microphallus. Sometimes micropenis occurs in boys who do not have enough of the male hormone testosterone.

Boys who do not have enough of this hormone are given supplements of testosterone.


Chordee is a curvature of the penis. The penis may bend downward, upward, or sideways or may be twisted. The bend may affect a boy's ability to direct the stream of urine while urinating.

If the bend is not severe, it may not need to be surgically corrected. If the bend is severe, surgery may be needed. People may choose to correct chordee if they are concerned it will affect their ability to have sexual intercourse or for cosmetic reasons.

Other defects of the penis

Some boys are born with a very tight frenulum (tissue located under the foreskin that helps pull the foreskin over the glans). A tight frenulum may prevent the foreskin from being completely pulled back over the tip of the penis. It may also cause pain or bleeding when the foreskin is pulled back or during an erection.

To treat the symptoms, doctors may surgically remove or cut the frenulum when the boy is older.

Drugs Mentioned In This Article

Generic Name Select Brand Names
testosterone DELATESTRYL

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