Atypical Genitalia (Formerly Known as Ambiguous Genitalia)

Atypical genitalia, formerly known as ambiguous genitalia, is a rare condition where your newborn’s external genitals don’t look typically male or typically female. Ambiguous genitalia (intersex genitals) is a difference of sexual development caused by hormonal irregularities during pregnancy. Treatment includes hormone therapy or surgery.


What is ambiguous genitalia (now known as atypical genitalia)?

Atypical genitalia, formerly known as ambiguous genitalia, is a rare disorder in which your newborn’s external genitals aren’t clearly defined. Your infant may not have the typical genitals of a male or a female. Your infant’s genitals may not have developed completely, or they may have features of both sexes.

Infants with atypical (intersex) genitals may have external genitals that don’t match their internal sex organs or genetic sex. Atypical genitalia is a difference of sexual development (DSD).


Cleveland Clinic is a non-profit academic medical center. Advertising on our site helps support our mission. We do not endorse non-Cleveland Clinic products or services. Policy

How common is atypical genitalia (ambiguous genitalia)?

Atypical genitalia occurs in about 1 out of every 1,000 to 4,500 births.

Symptoms and Causes

How do the sex organs normally form?

Your baby’s sex organs develop in three steps. First, your baby’s genetic sex is determined when the sperm fertilizes the egg. The female parent shares an X chromosome and the male parent shares either an X or a Y chromosome. Your baby will be assigned female at birth (AFAB) if an XX chromosome forms. Your baby will be assigned male at birth (AMAB) if an XY chromosome forms.

After your baby’s genetic sex is determined, your baby’s sex organs (gonads) form. A baby AFAB will develop ovaries, and a baby AMAB will develop testes. After that, your baby’s inner reproductive system (internal genitalia) and external genitals form. Hormones from the ovaries or testes shape your baby’s external genitals.

If the process unfolds differently, a difference of sexual development (DSD) can occur. Hormones cause differences of sexual development. Either parent can pass down these hormones, or they can have no clear cause.


What causes atypical genitalia (ambiguous genitalia)?

Hormonal irregularities during pregnancy generally cause atypical genitalia. These irregularities interfere with your fetus’s developing sex organs. Causes vary depending on the number or combination of sex chromosomes that are present.


With 46 XX DSD, your baby’s internal sex organs include ovaries and a uterus, but their external sex organs may resemble a penis and testicles. 46 XX occurs when your baby is exposed to too many male hormones (androgens) when their external genitals are forming. The most common cause of 46 XX DSD is a disorder called congenital adrenal hyperplasia (CAH). In this condition, your baby’s adrenal glands produce excessive amounts of androgens.


With 46 XY DSD, your baby’s internal sex organs are male but external sex organs are unclear. 46 XY occurs when your baby’s testes don’t develop properly, they don’t make enough testosterone or your baby’s body can’t use the testosterone correctly.

Disorders of gonadal differentiation

With disorders of gonadal differentiation, your baby’s sex organs don’t develop completely into testes or ovaries. Mixed gonadal dysgenesis means the sex organs (testes or ovaries) may not fully develop. Partial gonadal dysgenesis means your baby’s sex organs form only some testicular tissue and the testes won’t work properly. Gonadal dysgenesis means both gonads stay premature and they won’t develop into testes or ovaries.

Ovotesticular DSD

With ovotesticular DSD, your baby’s sex organs have ovarian and testicular tissue, or your baby has one ovary and one teste. This is very rare.

What does ambiguous genitalia (atypical genitalia) look like?

Ambiguous genitalia (atypical genitalia) will look different depending on the sex chromosomes affected. Ambiguous genitalia (atypical genitalia) in genetic females may have the following features:

  • An enlarged clitoris that looks like a small penis.
  • The urethral opening (where urine comes out) may not be in the typical place.
  • The “lips” of the vagina (labia) may be fused and look like a scrotum (a pouch that normally contains the testicles).
  • A lump of tissue within the labia that looks like a scrotum with testicles.

Ambiguous genitalia (atypical genitalia) in genetic males may have the following features:

  • A penis doesn’t form or is very small and looks like an enlarged clitoris.
  • The urethral opening (where urine comes out) may be at the base of the penis instead of the tip.
  • A small, separated scrotum that looks like labia.
  • Undescended testicles.

What are the symptoms of atypical genitalia (ambiguous genitalia)?

The most obvious sign of atypical genitalia is the presence of sex organs that don’t look like a typical penis or vagina. Other symptoms may include:

  • Hormonal imbalances.
  • Menstruation begins early, late or not at all.
  • Hypospadias. A condition that occurs when the urethral opening isn’t at the tip of the penis.


Diagnosis and Tests

How is ambiguous genitalia diagnosed?

Most babies receive a diagnosis of ambiguous genitalia at birth. When it’s unclear if your newborn is male or female, your baby’s healthcare provider will order further tests to determine a diagnosis.

What should I expect at my child’s appointment?

Your baby’s healthcare provider will ask about your family’s medical history and examine your baby’s external genitals. They may order several tests to determine the correct diagnosis. Your baby’s healthcare provider may order:

Sometimes, your baby’s healthcare provider can make a quick diagnosis, but sometimes it can take longer. A clear diagnosis is important for defining your baby’s sex and determining the correct treatment.

Management and Treatment

How is ambiguous genitalia (atypical genitalia) treated?

The first step of management is to identify the cause of atypical genitalia. Then, your baby’s healthcare provider will put together a treatment plan and sex assignment based on hormone tests and other test results.

You may work with a team of healthcare providers to help you make decisions about your baby’s sex and treatment. Make sure to seek out healthcare providers with expertise in this area. Experts in this area can help advise you on how best to proceed with treatment for your baby. Your team may include a:

Together with your baby’s healthcare providers, you’ll consider the correct treatment for your baby’s long-term well-being, gender identity and future sexual function and potential for fertility. Treatment depends on many factors, including:

  • The cause of your baby’s condition.
  • The appearance of your baby’s genitals.
  • Your family’s preferences and cultural beliefs.

Treatment options may include:

  • Hormone replacement therapy (HRT): Hormone therapy alone may help treat a hormonal imbalance.
  • Reconstructive surgery: Your baby’s healthcare team, in consultation with you, may suggest surgery while your baby is still an infant. But reconstructive surgery for atypical genitalia is controversial. Sometimes, it’s medically necessary, such as when your child is born without a urinary drainage opening. But if it’s more about appearance, some parents choose to forego surgery until their child is old enough to make the decision themselves.

Outlook / Prognosis

What can I expect if my child has ambiguous genitalia (atypical genitalia)?

Ambiguous genitalia (atypical genitalia) can have profound physical, social and psychological effects on your child. Your child’s genitals can shape the way they understand their gender. The decision to seek surgery can affect your child’s quality of life, which is why it’s a good idea to speak to a counselor who specializes in this area. While a diagnosis of ambiguous genitalia (atypical genitalia) can be distressing, your team of healthcare providers can help you determine the best possible course of treatment.

Living With

When should I seek care for my child’s atypical genitalia (ambiguous genitalia)?

Your baby’s healthcare provider usually discovers atypical genital (ambiguous genitalia) at birth or at their first well-child exam. Their healthcare provider will talk to you about diagnosis and treatment options.

What questions should I ask my child’s healthcare provider?

  • Does my child need treatment immediately, or can we wait and make a decision later?
  • What specialists should my child see?
  • Should we speak with a genetic counselor?
  • What will my child’s future look like?
  • Are there support groups for people with ambiguous genitalia (atypical genitalia)?

Additional Common Questions

Will my child be able to reproduce?

Future fertility and sexual function depend on the cause of ambiguous genitalia (atypical genitalia). Some studies have shown:

  • People AFAB with congenital adrenal hyperplasia can get pregnant after taking hormonal therapy.
  • People AMAB with at least one normal working testicle can be fertile.
  • People with ovotesticular DSD with a normal working ovary can be fertile.
  • People with testicular dysgenesis with a well-developed uterus can hold an implanted embryo.

Will my child have trouble with gender identity?

People AFAB with congenital adrenal hyperplasia usually understand their sexual identity and function well. People AMAB can understand their sexual identity and have successful sexual relations after hypospadias repair. However, ejaculation may be weaker than normal.

A note from Cleveland Clinic

A diagnosis of ambiguous genitalia (atypical genitalia) in your newborn can be very distressing for you and your family. You need to discuss many medical, ethical and psychological issues with your family and healthcare team. Your team of healthcare providers can provide the information and counseling you need to help you make decisions about your baby’s sex and treatment. This way, you can provide the best quality of life and achieve the best possible outcomes for your child.

Medically Reviewed

Last reviewed on 03/09/2022.

Learn more about our editorial process.

Call Appointment Center 866.320.4573
Questions 216.444.2200