Genital and urinary tract defects

Babies and birth defects

Key Points

Some babies are born with birth defects that affect sex organs (like the penis or vagina) and the urinary tract (like the kidneys or bladder).

We don’t know the exact cause of most genital and urinary tract defects.

Ask your provider about any medicines you take. Taking some medicines before or during early pregnancy may cause these birth defects in your baby.

Many genital and urinary tract defects can be diagnosed before birth with an ultrasound. Others may be diagnosed after birth with a physical exam.

Babies with genital and urinary tract defects often live healthy lives.

What are genital and urinary tract defects?

Genital and urinary tract defects are birth defects. Birth defects are structural changes present at birth that can affect almost any part of the body. They may affect how the body looks, works or both. Birth defects can cause problems in overall health, how the body develops or how the body works. About 1 in 500 babies is born with genital and urinary tract defects.

Genitals are sex organs. Some genitals, like the penis, are outside the body. Others, like the ovaries, are inside the body. The urinary tract is the system of organs (like the kidneys and bladder) that helps your body get rid of waste and extra fluids.

Babies with genital and urinary tract defects often live healthy lives. Your baby may only need regular visits with his health care provider.

What problems can genital and urinary tract defects cause?

Genital and urinary tract defects affect one or more of a baby’s body parts, including:

  • Kidneys, the pair of organs that remove waste from the blood and make urine
  • Bladder, the organ that holds urine
  • Ureters, two tubes that carry urine from the kidneys to the bladder
  • Urethra, the tube that carries urine out of the body from the bladder
  • Male genitals, including the penis and testicles. Testicles (also called testes) are two egg-shaped organs usually found in the sac (also called the scrotum) behind the penis. They make sperm and testosterone (a male hormone). In some boys, the testes are inside the belly instead of the scrotum. This condition is called undescended testes.
  • Female genitals, including the vagina, ovaries and uterus (also called womb)

Genital and urinary tract defects can cause:

  • Urinary tract infections (also called UTIs). These are infections in any part of the urinary tract. A UTI causes a burning feeling when you urinate (pee).
  • Pain
  • Kidney damage
  • Kidney failure. This is a serious condition that happens when the kidneys don’t work well and allow waste to build up in the body.

How do you know if your baby has a genital and urinary tract defect?

Some of these birth defects can be diagnosed before birth with an ultrasound. Ultrasound uses sound waves and a computer screen to show a picture of your baby inside the womb. Others may be diagnosed during your baby’s checkup in the hospital nursery after birth.

Your baby gets tested for a condition called congenital adrenal hyperplasia (also called CAH) as part of newborn screening after birth. Newborn screenings check for serious but rare and mostly treatable conditions at birth. It includes blood, hearing and heart screenings. CAH is a group of genetic disorders that affect the adrenal glands. The adrenal glands sit on top of the kidneys and make hormones. Babies with CAH have trouble making enough of certain hormones and too much of other hormones. CAH can affect how a baby’s genitals develop. This can cause a baby girl’s genitals to look like a baby boy’s genitals. It also can cause a boy or girl to start puberty at a young age. Puberty is the time in your life when your body develops and changes from being a child to an adult.

If your baby’s health care provider thinks your baby may have a urinary tract defect, she may use a test called voiding cystourethrogram to check your baby. In this test, your baby’s provider inserts a catheter (a thin, flexible tube) into your baby’s bladder through the urethra. Contrast dye flows through the catheter and fills the bladder. This dye helps the bladder show up better on X-ray images. X-ray is a medical test that uses radiation to make a picture of your baby’s body on film.

X-rays are taken of your baby’s bladder while it’s full of the contrast dye. Your baby’s provider removes the catheter so your baby can pee and X-rays take more images of your baby while he empties his bladder. Your baby’s provider uses these images to check that your baby’s bladder and urethra are working well.

Do babies with genital and urinary tract defects need special medical care?

You and your baby may have a team of providers who treat these birth defects and help you with related concerns. The team may include:

 Doctors, including:

  • An endocrinologist treats hormone problems
  • A maternal-fetal medicine specialist (also called MFM) has special education and training to take care of women who have high-risk pregnancies
  • A neonatologist takes care of sick newborns, including premature babies (born before 37 weeks of pregnancy) and babies with birth defects
  • A pediatrician treats babies and children
  • A pediatric gastroenterologist treats the digestive system in babies and children
  • A pediatric surgeon has special training doing surgery on babies and children
  • A psychiatrist treats people with emotional or mental health problems, like depression
  • A urologist treats problems of the urinary tract

Other kinds of providers, including:

  • A genetic counselor is trained to help you understand about genes, birth defects and other medical conditions that run in families, and how they can affect your health and your baby’s health
  • A social worker is a mental health professional who helps people solve problems and make their lives better.

What are ambiguous genitals?

In a baby with ambiguous genitals, the genitals outside the body (the penis or vagina) aren’t clearly either male or female. About 1 in 4,500 babies (less than 1 percent) has ambiguous genitals.

Ambiguous genitals are a common sign of several disorders of sexual development (also called DSDs). These are conditions in which a baby’s genitals outside the body are different from what a baby’s chromosomes (XX for females, XY for males) or organs inside the body say they should be. In most cases, having ambiguous genitals is not life-threatening. Babies and children with these conditions may have hormone replacement treatment or surgery on the genitals.

What are bladder exstrophy-epispadias complex defects and how are they treated?
Bladder exstrophy-epispadias complex defects are a group of birth defects (also called BEEC defects). They include:

Bladder exstrophy. This is the most common BEEC defect. About 1 in 50,000 babies is born with the condition each year in the United States. Bladder exstrophy happens when the bladder is turned inside out and bulges outside of the belly. It can involve other parts of the body, including the urinary tract, muscles, bones and the reproductive and digestive systems. The condition is slightly more common in boys than in girls. Babies with bladder exstrophy have surgical procedures to repair the affected organs, muscles and bones.

Babies with bladder exstrophy also have a condition called vesicoureteral reflux. This happens when urine flows backward through the ureter from the bladder up into the kidney. Urine usually only flows one way through the ureter. When urine flows the wrong way, the kidney has trouble emptying correctly. Sometimes vesicoureteral reflux gets better and goes away as a child gets older. If not, a child’s treatment for this condition may include:

  • Surgery to remove a blockage or correct an abnormal bladder or ureter
  • Antibiotics to treat UTIs. Antibiotics are medicines that kill certain infections.
  • Intermittent urinary catheterization. During this procedure, your child’s provider inserts a catheter through the urethra to the bladder. You also can do this procedure at home if your child’s bladder doesn’t empty properly.

Epispadias. This is the least severe of the BEEC defects. Epispadias is a defect in the urethra that often happens with bladder exstrophy. It can cause these problems:

  • For boys, a shorter-than-normal urethra with an opening on the upper part of the penis instead of the penis tip
  • For boys, a penis that looks short and flat and may curve upward
  • For girls, a clitoris that is split and, sometimes, the urinary opening in the wrong place. The clitoris is a female external sex organ.
  • For boys and girls, bladder control problems
  • For boys and girls, wide pelvic bones and rotated hips. The pelvic bones form the base of the spine and the socket of the hip joint.

Some babies with epispadias need surgery to help treat problems with bladder control and how the genitals look and work. Surgery is usually done 6 to 12 weeks after birth. Your baby needs checkups with a health care provider as he grows.

Cloacal exstrophy. This is the most serious form of BEEC. About 1 in 250,000 babies are born with this condition each year in the United States. Cloacal exstrophy happens as a baby’s lower abdominal (belly) wall develops in the womb. In babies with this condition, the rectum, bladder and genitals do not fully separate as the baby grows and these organs may not develop properly. Part of the large intestine may be outside a baby’s body, with each half of the bladder on either side of the intestine. In boys, the penis is often flat and each half of the penis is separated. In girls, the clitoris is split into two halves.

Cloacal exstrophy also can affect the pelvic bones, backbone, spinal cord and kidneys. The spinal cord is a bundle of nerves that runs down the middle of your back. It carries signals back and forth between your body and your brain. Most babies born with cloacal exstrophy have problems with their spine, like spina bifida. Spina bifida happens when the spinal cord or bones in the spine don’t form correctly, leaving a gap or opening. Spina bifida can happen anywhere along the spine. Babies and children with spina bifida may have health and development problems, including fluid on the brain, being paralyzed and having learning and developmental disabilities.

Babies with cloacal exstrophy need a staged reconstruction to repair the affected organs. A staged reconstruction involves a series of surgeries that are done over several years. The types of surgery involved and timing of them depend on your baby’s condition.

What is hydronephrosis and how is it treated?

In hydronephrosis, one or both kidneys swell because a blockage in the urinary tract causes urine to back up into the kidneys. It affects up to 1 in 100 (1 percent) pregnancies.

When hydronephrosis happens to a baby in the womb, it’s called fetal hydronephrosis. It usually goes away without lasting problems. However, sometimes the blockage can damage the kidneys or become life-threatening for a baby. If hydronephrosis is diagnosed before birth with ultrasound, your health care provider checks your baby with repeat ultrasounds throughout your pregnancy to see if it goes away or gets worse. Most babies don’t need treatment until after birth. But if hydronephrosis becomes life-threatening before birth, you may need to give birth early or have surgery to put a shunt (small tube) into your baby’s bladder while he is still in the womb. The shunt drains urine into the amniotic fluid until birth.

After your baby’s born, he may get a type of X-ray called a renal scan. In this test, your baby’s provider puts a small amount of radioactive substance called a tracer into your baby’s vein. A special gamma camera tracks the tracer as it moves through the body and creates images on a computer screen. This helps your baby’s health care provider see how the body works. Your baby’s provider times how long it takes the kidneys to pass the tracer to find out how well they’re are working. This test is usually done several weeks after birth.

After birth, mild hydronephrosis may go away without treatment. If the blockage doesn’t go away, your baby may need surgery.

What is hypospadias and how is it treated?

Hypospadias is a condition that affects only boys. It’s when the opening of the urethra is on the underside of the penis instead of at the tip of the penis. Hypospadias affects at least 5 in 1,000 (less than 1 percent) baby boys.

Boys with this condition may have a curved penis. This may cause them to have problems with spraying urine, so they may need to sit down to urinate. In some boys, the testicles also don’t fully drop down into the scrotum before birth. Without treatment, hypospadias can lead to problems with sex and urinating while standing.

Hypospadias usually is diagnosed in baby boys during a physical exam after birth. Most babies need surgery to correct the condition. If surgery is needed, it’s usually done when the baby is 3 to 18 months old. If you plan to have your son circumcised, you may need to wait because your baby’s health care provider may use the penis foreskin in surgery to help fix hypospadias. Circumcision is a surgical procedure that removes foreskin from the penis. Foreskin is the fold of skin that covers the tip of the penis.

Most babies are diagnosed with hypospadias while still in the hospital after being born. Tell baby’s health care provider if your son’s penis looks unusual or if he has problems urinating when you’re home from the hospital.

What is kidney dysplasia and how is it treated?

Kidney dysplasia (also called renal dysplasia or multicystic dysplastic kidney) is a condition that happens when which cysts (fluid-filled sacs) grow inside of one or both kidneys. The cysts may appear to replace one or both kidneys. A blockage in a baby’s urinary tract early in pregnancy may cause kidney dysplasia. It affects about 1 in 4,000 babies (less than 1 percent) but some babies are never diagnosed with the condition.

Kidney dysplasia usually happens in only one kidney. In these cases, babies have few, if any, health problems. However, if it affects both kidneys, babies may not survive pregnancy because there may not be enough amniotic fluid surrounding the baby and the baby’s lungs may be affected. Babies who do survive need dialysis and a kidney transplant very soon after birth. Dialysis is a treatment that filters your blood to rid your body of harmful wastes, extra salt and water.

Other complications of kidney dysplasia can include:

  • Hydronephrosis of the normal kidney
  • UTIs
  • High blood pressure
  • A slightly increased chance of getting kidney cancer

Health care providers often find kidney dysplasia during an ultrasound. After birth, your baby’s provider may diagnose it during an exam for a urinary tract infection or other medical condition. Your baby needs regular checkups to test for high blood pressure and kidney damage.

What is polycystic kidney disease and how is it treated?

Polycystic kidney disease (also called PKD) is a condition that causes cysts to grow in the kidneys. The cysts make the kidneys work poorly, leading to kidney failure. Cysts also may develop in other organs, like the liver. There are two major forms of PKD:

  1. Autosomal dominant PKD. This is the more common form. It usually happens when a baby inherits the PKD gene change from a parent. A gene change (also called a mutation) is a change to instructions that are stored in a gene. The change sometimes can cause birth defects and other health conditions. A gene can change on its own, or it can be passed from parents to children. However, 1 in 10 people with autosomal dominant PKD doesn’t have a family history of PKD. Symptoms usually appear in adulthood, but some children have symptoms. This type of PKD affects between 1 in 500 and 1 in 1,000 people (less than 1 percent).
  2. Infantile or autosomal recessive PKD. This is rare and happens when both parents (who aren’t affected by PKD themselves) pass the PKD gene change to their child. Cysts may develop before birth and can be life-threatening. Symptoms also can appear later in childhood. Up to 1 in 25,000 babies (less than 1 percent) is born with this form of PKD. It can be diagnosed before your baby is born or shortly after birth. Symptoms include larger-than-normal kidneys and a smaller-than-normal baby, but some babies don’t have symptoms until later in life.

PKD treatments include:

  • Blood pressure medicines, diuretics (medicine that helps your body get rid of salt and water) and a low-salt meal plan
  • Antibiotics to treat urinary tract infections.
  • Draining cysts that are painful, infected, bleeding or causing a blockage
  • Dialysis
  • Surgery to remove one or both kidneys. If both kidneys are removed, your baby may need dialysis or a kidney transplant. This is surgery to place a healthy kidney into a person with kidney failure.

What is renal agenesis and how is it treated?

There are two kinds of renal agenesis:

  1. Unilateral renal agenesis. This is when a baby is born with just one kidney instead of two. Most babies with this condition grow and develop normally. However, some have other urinary tract defects that may cause problems for the one kidney. Health care providers can use ultrasound and other tests to check for problems that need special care. Between 1 in 450 and 1 in 1,000 babies (less than 1 percent) is born with this condition.
  2. Bilateral renal agenesis. This is when a baby is born without kidneys. Babies with this condition often die in the first days of life. To help a baby be healthier when he is born, health care providers may use treatments during pregnancy, like serial amnio infusion, to try to help the baby’s lungs develop before birth. These treatments are very specialized and are still being researched. Talk to your provider to find out if these treatments may help your baby. After birth, the baby needs dialysis. About 1 in 3,000 babies (less than 1 percent) is born with this condition.

What causes genital and urinary tract defects?

We don’t know the exact cause of most of these conditions, but there are some things that may make you more likely than other women to have a baby with genital and urinary tract defects.  These are called risk factors. Having a risk factor doesn’t mean for sure that your baby will be affected. But it may increase your chances.

Talk to your provider about things you can do to help reduce your risk for having a baby with genital and urinary tract defects. Risk factors for these birth defects may include:

Age and weight. Some research from the Centers for Disease Control and Prevention (CDC) suggests that women who are 35 or older and obese may have an increased risk of having a baby with hypospadias. Being obese means being very overweight with a body mass index (also called BMI) of 30 or higher. To find out your BMI, go to Eating healthy foods and being active every day can help you get to a healthy weight before pregnancy.

Contact with pesticides and industrial chemicals during pregnancy. Some experts think that exposure to pesticides and industrial chemicals during pregnancy may be linked to hypospadias. Pesticides are chemicals used to kill things like bugs, rodents, mold or weeds. More research is needed, but it’s best to avoid contact with these chemicals during pregnancy.

Family history of genital and urinary tract defects. Genes are parts of your body’s cells that store instructions for the way your body grows and works. Genes are passed from parents to children. If you or your partner has a family history of genital and urinary tract defects, or you have a child with one of these birth defects, you may want to talk with a genetic counselor before getting pregnant. Gene mutations and problems with chromosomes also may cause some genital and urinary tract defects, like ambiguous genitals.

Having hormones problems during pregnancy. If you have a disease or condition that causes your body to make too much male hormone, your baby may have ambiguous genitalia. In rare cases, a pregnant woman may have a tumor that makes male hormones and causes ambiguous genitals in her baby. If you have a condition that causes hormone problems before pregnancy, work with your health care provider to manage your condition and plan for pregnancy.

Smoking or using street drugs (like cocaine) during pregnancy. More research is needed, but doing these things during pregnancy may increase your risk of having a baby with a genital and urinary tract defect. Tell your health care provider if you need help to quit smoking or quit using drugs.

Taking certain medicines before and during pregnancy. Talk to you provider about any prescription medicines and over-the-counter medicines, supplements and herbal products you take. Taking some medicines just before you get pregnant or during early pregnancy may increase your risk of having a baby with a genital and urinary tract defect. You may need to stop taking a medicine or switch you to one that’s safer during pregnancy. For example:

  • Taking medicines to treat seizures and high blood pressure during pregnancy may cause kidney dysplasia in a baby.
  • Women who take progestins right before or during early pregnancy may be at increased risk of having a baby with hypospadias. Progestin is a form of progesterone, a hormone that helps your uterus grow during pregnancy and keeps it from having contractions.
  • Using fertility treatment to help you get pregnant. For example, using assisted reproductive technology (also called ART) may increase your risk of having a baby with hypospadias. ART is any kind of fertility treatment where both the egg and sperm are handled in a lab.
  • Taking a medicine that contains male hormones during pregnancy. This may cause a baby’s developing female genitals to become more like male genitals.

More information

Last reviewed: June, 2019