As babies develop in the womb, a tube forms that connects their developing bladder to each kidney. These tubes will become the ureters. They should be hollow to allow urine to pass through them from the kidney down to the bladder, and they have a wall that is made of smooth muscle.

Most cases of PUJ dysfunction happen because there is a problem with the development of this muscular wall and so part of the tube becomes very narrow. This narrowing causes a blockage.

In rare cases, the tube is compressed by something outside of it such as a blood vessel.