Genital and urinary tract defects

Genital and urinary tract defects are birth defects. Birth defects are health conditions that are present at birth that change the shape or function of one or more parts of the body. They can cause problems in overall health, how the body develops, or in how the body works.

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.

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 sac 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 (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 (womb)

Genital and urinary tract defects can cause:

  • Urinary tract infections (UTIs)
  • 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.

What causes genital and urinary tract defects?

We don’t know the exact cause of most of these conditions. But some happen when parents who have the condition, or carry the gene for the condition, pass it to their children. Genes are a part of your body’s cells that stores instructions for the way your body grows and works.

If you already have a child with a genital or urinary tract defect and are thinking about having another baby, you may want to speak with a genetic counselor. This is a person who is trained to help you understand about how genes, birth defects and other medical conditions run in families, and how they can affect your health and your baby's health.

How do you know if your baby has one of these conditions?

Many urinary tract 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. After birth, genital defects often are diagnosed during your baby’s checkup in the hospital nursery.

Your baby gets tested for a condition called congenital adrenal hyperplasia (also called CAH) as part of newborn screening after birth. Newborn screening checks for serious but rare and mostly treatable conditions. It includes blood, hearing and heart screening.

What are some common genital and urinary tract defects and how are they treated?

Common genital and urinary tract defects include:

Ambiguous genitals. In this condition, a baby’s genitals outside the body, like the penis or vagina, aren’t obviously 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. Treatment for these conditions may include hormone treatment or surgery on the genitals.

Bladder exstrophy and epispadias. Bladder exstrophy is 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 digestive system. This condition affects about 1 in 30,000 babies (less than 1 percent). It happens in boys slightly more often than girls.

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’s 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

Some babies need surgery to help treat problems with bladder control and how the genitals look and work.

Hydronephrosis. In this condition, 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 your baby in the womb, it’s called fetal hydronephrosis. It usually goes away without lasting problems. But sometimes the blockage can damage the developing kidneys or become life-threatening for your baby. If hydronephrosis is diagnosed before birth with ultrasound, your provider checks your baby with repeat ultrasounds 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 still in the womb. The shunt drains urine into the amniotic fluid until birth. After birth, mild hydronephrosis may go away without treatment. If the blockage doesn’t go away, your baby may need surgery.

Hypospadias. This condition 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. Hyposadias affects at least 1 in 300 baby boys (less than 1 percent).

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. And in some boys, the testicles don’t fully drop down into the scrotum before birth. Without treatment, hyposadias can lead to problems with sex or urinating later in life.

Hypospadias usually is diagnosed in baby boys during a physical exam after birth. Most babies need surgery to correct the condition. If you plan to have your son circumcised, you may need to wait because your baby’s 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.

Kidney dysplasia (also called renal dysplasia or multicystic dysplastic kidney). In this condition, cysts grow inside of one or both kidneys. The cysts may appear to actually 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 2,000 babies (less than 1 percent).

Kidney dysplasia usually happens in only one kidney. In these cases, babies have few, if any, health problems. But if it affects both kidneys, babies may not survive pregnancy. Babies who do survive need dialysis and a kidney transplant very soon after birth.

Kidney dysplasia is often found during an ultrasound. After birth, it may be found during an exam for a urinary tract infection or other medical condition.

Polycystic kidney disease (also called PKD). This condition causes cysts (fluid-filled sacs) 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 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. But 1 in 10 (10 percent) people with autosomal dominant PKD don’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. Autosomal recessive PKD 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 20,000 babies (less than 1 percent) is born with this form of PKD.

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. Antibiotics are medicines that kill infections caused by bacteria.
  • Draining cysts that are painful, infected, bleeding or causing a blockage
  • Dialysis. This treatment filters your blood to rid your body of harmful wastes, extra salt and water.
  • Surgery to remove one or both kidneys. If both kidneys are removed, you need dialysis or a kidney transplant. This is surgery to place a healthy kidney into a person with kidney failure.

Renal agenesis. There are two kinds of renal agenesis:

  1. Unilateral renal agenesis is when a baby is born with just one kidney instead of two. Most babies with this condition grow and develop normally. But some have other urinary tract defects that may cause problems for the one kidney. 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 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 born healthier, providers may use treatments during pregnancy, like serial amnio infusion, to try to help the baby's lung's 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. For more more information, visit

See also:
Genetic counseling

Last reviewed: February, 2013