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:

• An enlarged clitoris, which may look like a penis.
• Closed labia, or labia that include folds and look like a scrotum.
• Lumps that feel like testicles in the fused labia.

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

• A condition in which the narrow tube that carries urine and semen, called the urethra, doesn't fully extend to the tip of the penis. If the tube opening is on the underside of the penis, the condition is called hypospadias.
• A very small penis with the urethral opening closer to the scrotum.
• One or both testicles missing in what appears to be the scrotum.
• Testicles that remain in the body, also called undescended testicles, and an empty scrotum that has the appearance of labia with or without a micropenis.

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.

• In a fetus with a Y chromosome, a region on that chromosome triggers the development of testicles, which make androgens. Male genitals develop in response to these hormones from the fetal testicles.
• In a fetus without a Y chromosome, and without the effects of androgens, the genitals develop as female.

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.

• If a genetic male fetus doesn't make hormones called androgens or doesn't have enough of these hormones, it can cause atypical genitalia. Exposure to androgens during development in a genetic female fetus results in atypical external genitalia.
• Changes in certain genes can affect fetal sex development and cause atypical genitalia.
• Atypical genitalia also can be a feature of certain rare or complex syndromes that affect many organs. These syndromes can include chromosome changes such as a missing sex chromosome or an extra one.

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:

• Congenital adrenal hyperplasia. Certain forms of this genetic condition cause the adrenal glands to make too much of hormones called androgens.
• Exposure to certain hormones before birth. Some drugs that contain androgens or that cause a pregnant person's body to make these hormones can cause developing female genitals to become more masculine. A developing fetus also may be exposed to too much of the hormones that cause the development of male genitals if the pregnant person has a condition that causes hormones to be out of balance.
• Tumors. Rarely, a tumor in the pregnant person can make hormones that cause the development of male genitals.

Possible causes in genetic males

Causes of atypical genitalia in genetic males may include:

• Problems with testicle development. This may be due to changes in genes or due to unknown causes.
• Androgen insensitivity syndrome. In this condition, developing genital tissues don't respond as they should to hormones made by the testicles.
• Problems with the testicles or testosterone. A variety of problems can interfere with the testicles' activity. These can include problems with how the testicles are formed and problems with making the hormone testosterone. This also may include problems with certain proteins in cells that tell the cells to respond to testosterone.
• 5-alpha-reductase deficiency. Not having enough of this enzyme causes problems with making hormones that cause the development of male genitals.

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:

• Unexplained deaths in early infancy.
• Infertility, not having menstrual periods or having a lot of facial hair in females.
• Atypical genitalia.
• Atypical physical development during puberty.
• Congenital adrenal hyperplasia, a group of genetic conditions that affect the adrenal glands and are passed down in families.

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:

• Infertility. Whether people with atypical genitalia can have children depends on the specific diagnosis. For example, genetic females with congenital adrenal hyperplasia usually can get pregnant if they so choose.
• Higher risk of certain cancers. Some differences of sex development are linked with a higher risk of certain types of cancer.

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:

• Blood tests to measure hormone levels.
• Blood tests to look at chromosomes. This can show the genetic sex: typically, XX or XY. These blood tests also can show conditions caused by a gene change that affects sex organ development.
• Ultrasound of the pelvis and belly to look for testicles that haven't descended, a uterus or a vagina.
• X-ray studies using a contrast dye to help give a clear picture of pelvic and belly structures.

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:

• Pediatricians.
• Experts in newborns born early or with medical conditions, also called neonatologists.
• Experts in children's urinary systems, also called pediatric urologists.
• Pediatric general surgeons.
• Experts in the body's hormones, also called endocrinologists.
• Medical geneticists.
• Mental health professionals, such as psychologists or social workers.

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:

• Keep healthy sexual function.
• Create genitals that appear more typical.

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:

• Ask if there's anything you need to do to prepare your baby for tests and procedures.
• Discuss family history with your blood relatives, such as parents, grandparents and cousins, and bring key personal information, including family history of genetic conditions, such as atypical genitalia.
• Consider taking a family member or friend along. Sometimes it can be hard to remember all the information given during an appointment. Someone who goes with you may remember something that you missed or forgot.
• Make a list of questions to ask your healthcare professional.

Questions to ask may include:

• What caused my baby's atypical genitalia?
• What genetic testing has been done?
• What other tests might my baby need?
• What is the best treatment plan?
• What are other options to the primary treatment that you're suggesting?
• Is there a generic option to the medicine you're prescribing?
• Are there any special instructions that I need to follow?
• Should my baby see any other specialists?
• What options are there for counseling and support for our family?
• Do you have any printed material that can help me learn more? What websites do you suggest?

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:

• Does your family have a history of atypical genitalia?
• Does your family have a history of genetic conditions?
• Do any health conditions tend to run in your family?
• Have you ever had a miscarriage?
• Have you ever had a child who died in infancy?

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