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Atypical genitalia

Atypical genitalia, formerly called ambiguous genitalia, is a rare condition in which an infant’s genitals don’t appear to be clearly male or female on the outside. In a baby with atypical genitalia, the genitals may not be developed fully or may look different from what is expected. Or the baby may have features of more than one sex. The sex organs on the outside of the body may not match the sex organs on the inside. And they may not match the genetic sex, which is determined by sex chromosomes: typically, XX for females and XY for males.

External genitals are the sex organs on the outside of the body. They include the opening of the vagina and the labia, clitoris, penis and scrotum. Internal genitals are the sex organs inside the body. They include the vagina, fallopian tubes, uterus, prostate, ovaries and testicles. Sex hormones are made by the ovaries and testicles, which also are called gonads. Genetic sex is set based on sex chromosomes. Typically, these sex chromosomes are a genetic female with two X chromosomes and a genetic male with one X and one Y chromosome.

Atypical genitalia is not a disease; it’s a difference of sex development. Usually, atypical genitalia can be seen at or shortly after birth. The condition can be very distressing for families. Your medical team looks for the cause of atypical genitalia and provides information and counseling that can help guide decisions about your baby’s sex and any needed treatment.

Your medical team will likely be the first to notice atypical genitalia soon after your baby is born. Sometimes, atypical genitalia may be suspected before birth. Atypical genitalia can vary in appearance. Differences may depend on when during genital development the hormone changes that affected development occurred and the cause.

Babies who are genetically female, which means they have two X chromosomes, may have:

Babies who are genetically male, which means they have one X and one Y chromosome, may have:

Atypical genitalia usually happen when hormone changes during pregnancy stop or disturb an unborn baby’s developing sex organs. An unborn baby also is called a fetus.

How sex organs form in the womb

A baby’s genetic sex is set at conception, based on the sex chromosomes. Conception is when the egg from one parent meets the sperm from the other parent. The egg contains an X chromosome. The sperm contains either an X or a Y chromosome. A baby who gets the X chromosome from the sperm is a genetic female with two X chromosomes. A baby who gets the Y chromosome from the sperm is a genetic male with one X and one Y chromosome.

Male and female sex organs develop from the same tissue. Whether this tissue becomes male organs or female organs depends on the chromosomes and the presence or absence of hormones called androgens. Androgens cause the development of male genitals.

Sometimes a chromosomal change may make it hard to figure out the genetic sex.

How atypical genitalia occurs

A change in the steps that influence fetal sex development can result in a mismatch between the appearance of a baby’s external genitals and the baby’s internal sex organs or genetic sex, typically XX or XY.

Sometimes it’s not possible to find the cause of atypical genitalia.

Possible causes in genetic females

Causes of atypical genitalia in genetic females may include:

Possible causes in genetic males

Causes of atypical genitalia in genetic males may include:

Family history may play a role in the development of atypical genitalia. This is because many differences of sex development result from gene changes that can be passed down in families. Possible risk factors for atypical genitalia include a family history of:

If your family has a history of these risk factors, talk with your healthcare professional before trying to get pregnant. Genetic counseling also can help in planning ahead.

Complications of atypical genitalia may include:

Atypical genitalia is usually diagnosed at birth or shortly after. Sometimes, healthcare professionals may suspect atypical genitalia during pregnancy when results of blood tests of the unborn baby’s sex differ from the ultrasound imaging of the baby’s genitalia. But generally, the diagnosis is not made until after birth. Healthcare professionals who help with delivery may notice the signs of atypical genitalia in your newborn.

Determining the cause

If your baby is born with atypical genitalia, your doctor and other healthcare professionals work to find the cause. The cause helps guide treatment and decisions about your baby’s sex. Your healthcare professional begins by asking questions about your family and medical history. Your baby has a physical exam to check for testicles and evaluate the genitalia.

Your baby will likely have these tests:

Sometimes minimally invasive surgery is needed to collect a tissue sample of your newborn’s reproductive organs. This surgery is done through one or more small cuts using tiny cameras and surgical tools.

Deciding the sex

Using the information gathered from these tests, your healthcare professional may suggest a sex for your baby. The suggestion is based on the cause, genetic sex, anatomy, future reproductive and sexual potential, probable adult gender identity, and discussion with you.

Sometimes, a family may make a decision within a few days after the birth. But it’s important that families wait until tests are finished. Sex assignment can be complex and delayed. Parents should be aware that as the child grows up, the child may make a different decision about gender identification.

The goal of treatment is long-term mental health and social well-being, as well as having as much sexual function and fertility as possible. When to begin treatment depends on your child’s specific situation.

Atypical genitalia is complex and not common. Managing it may require a team of experts. The team might include:

Medicines

Hormone medicines may help correct or manage hormones that are out of balance. For example, in a genetic female with a slightly enlarged clitoris caused by mild congenital adrenal hyperplasia, hormone replacement maybe the only treatment needed.

Surgery

In children with atypical genitalia, surgery may be used to:

The timing of surgery depends on your child’s specific situation. Some healthcare professionals prefer to postpone surgery done only for appearance. They suggest waiting until the person with atypical genitalia is mature enough to be part of the decision about sex assignment.

For children with atypical genitalia, the sex organs may work properly in spite of how the genitals look on the outside. For girls, if the vagina is hidden under the skin, for example, surgery in childhood can help with sexual function later. For boys, surgery to reconstruct a partially developed penis may create a more typical appearance and make erections possible. Surgery to move the testicles into the scrotum may be needed.

Results of surgery are often satisfying. But repeat surgeries may be needed. Risks include a disappointing appearance or problems with sexual function, such as trouble reaching an orgasm.

Ongoing care

Children with atypical genitalia need ongoing medical care. This includes watching for complications, such as getting cancer screenings into adulthood.

If your baby has atypical genitalia, you may worry about the baby’s future. Mental health professionals can help you deal with this difference that you didn’t expect. Ask your child’s healthcare professional for a referral to a mental health professional who has experience helping people in your situation. You also may find it helpful to join a support group, either in person or online.

Your child may find ongoing counseling by mental health professionals helpful and may choose to be a part of support groups into adulthood.

Not knowing the sex of your newborn right away might turn a hoped-for celebration into a stressful time. Your medical team can provide you with updates and information as quickly as possible. They also can answer questions and talk with you about your child’s health.

Consider waiting to make a formal announcement of the birth until testing is done and you’ve created a plan with advice from your medical team. Give yourself some time to learn and think about your child’s condition before answering questions from family and friends.

If your baby is born with atypical genitalia, you may be referred to a medical center with doctors and other healthcare professionals who have expertise in managing this condition. Here’s some information to help you get ready for your appointment and learn what to expect.

What you can do

Before your appointment:

Questions to ask may include:

Feel free to ask other questions during your appointment.

What to expect from your doctor

Your healthcare professional is likely to ask you questions, such as:

Be ready to answer questions so that you have time to talk about what’s most important to you.

© 1998-2024 Mayo Foundation for Medical Education and Research (MFMER). All rights reserved.

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