“Holes” in the kidneys almost always refer to cysts, which are fluid-filled sacs that develop within or on the kidney tissue. They can also describe cavities from infection, tissue death from blocked blood flow, or the sponge-like appearance of a congenital condition called medullary sponge kidney. The cause depends entirely on the type of “hole,” and most of them are harmless.
Simple Kidney Cysts
The most common cause of hole-like structures in the kidneys is simple renal cysts. These are round, fluid-filled pockets that form on or inside the kidney, and they become increasingly common with age. About 4% of people under 30 have them, but that number climbs to roughly 33% by age 60 and older. Men develop them more often than women.
Simple cysts grow slowly, averaging about 5% per year in diameter. At that rate, a cyst can grow to 1.6 times its original size over a decade. Most never cause symptoms and are discovered by accident during imaging for something else. In rare cases, a large cyst can press on surrounding tissue and cause flank pain, block urine flow, become infected, or burst. A ruptured cyst can cause sudden pain and blood in the urine. Some cysts have also been linked to high blood pressure.
When a simple cyst does cause problems, treatment typically involves either draining it with a needle and filling the space with a scarring solution to prevent it from refilling, or surgically removing it through small incisions. Both are uncommon, because most simple cysts never need treatment at all.
Polycystic Kidney Disease
Polycystic kidney disease (PKD) is a genetic condition where thousands of cysts form in both kidneys, gradually enlarging them and crowding out healthy tissue. Unlike simple cysts, PKD is progressive and can lead to kidney failure.
The most common form, autosomal dominant PKD, is caused by mutations in one of two genes (PKD1 or PKD2). These genes produce proteins that help kidneys develop and organize normally. When the genes are faulty, cells in the kidney lining grow abnormally and form fluid-filled sacs that multiply over decades. A parent with the condition has a 50% chance of passing it to each child. A rarer form, autosomal recessive PKD, involves a different gene and typically appears in infancy or childhood.
PKD cysts are far more numerous and destructive than simple cysts. They disrupt the kidney’s filtering ability and can also affect the liver and other organs.
Medullary Sponge Kidney
Medullary sponge kidney is a congenital condition where the tiny collecting tubes deep inside the kidney become abnormally widened, forming clusters of small cysts between 1 and 8 millimeters across. When the kidney is cut open, the affected area looks like a sponge, full of small holes filled with clear, jelly-like material.
The condition is present from birth, though it often goes undetected until adulthood. The dilated tubes tend to trap calcium, making kidney stones a frequent complication. Many people with medullary sponge kidney experience recurrent stones or urinary tract infections before the underlying condition is ever identified. On its own, it rarely threatens kidney function.
Acquired Cystic Kidney Disease
People with long-standing kidney failure, particularly those on dialysis, develop a distinct condition called acquired cystic kidney disease (ACKD). Unlike other cystic conditions, ACKD is not genetic. It develops as a direct consequence of the kidneys shrinking and scarring over time.
The longer someone is on dialysis, the more likely they are to develop ACKD. Within the first three years, roughly 10% to 20% of dialysis patients have it. By five years, that rises to 40% to 60%. After nine or more years on dialysis, over 90% of patients show cysts. The concern with ACKD is that it carries an elevated risk of kidney cancer, so people on long-term dialysis are typically screened with imaging on a regular basis.
Kidney Abscesses
A severe kidney infection can destroy a pocket of tissue and leave behind a cavity filled with pus. This is a kidney abscess, and on imaging it can look like a hole or a dark mass within the organ. Abscesses usually develop as a complication of a serious urinary tract infection (pyelonephritis) or from bacteria that travel to the kidney through the bloodstream.
On a CT scan, an abscess appears as an irregular mass with thick walls and a fluid-filled center. Unlike cysts, abscesses cause obvious symptoms: fever, significant pain, and tenderness over the affected kidney. They require aggressive treatment, often drainage and a prolonged course of antibiotics.
Blood Flow Blockages and Tissue Death
When blood supply to part of the kidney is suddenly cut off, the affected tissue dies. This is called renal cortical necrosis or renal infarction, depending on the pattern. On imaging, the dead tissue appears as areas that don’t light up with contrast dye, creating dark patches that can resemble holes or thinned-out zones.
This type of damage can happen after severe blood loss, dangerously low blood pressure, blood clots, sepsis, or certain pregnancy complications like eclampsia. The necrosis can be patchy, affecting scattered sections of the kidney’s outer layer, or diffuse, destroying large swaths of tissue while sparing only a thin rim near the capsule. Either pattern results in permanent scarring and, in severe cases, kidney failure.
When a Cyst Might Be Cancerous
Most kidney cysts are completely benign, but some have features that raise concern. Doctors use a grading system (called the Bosniak classification) to sort cysts based on how they look on imaging. A simple, thin-walled cyst with no internal structures scores at the lowest level, with a 0% chance of being cancerous. At the other end, a cyst with thick, irregular walls and solid components that take up contrast dye has about a 62% chance of being malignant.
The middle categories carry intermediate risk. Minimally complex cysts have a malignancy rate under 2%, while moderately complex cysts that need monitoring over five years sit around 4%. Cysts that show thickened walls, internal separations, or areas of enhancement jump to about 28%. Your doctor uses these features to decide whether a cyst can be safely left alone, needs periodic imaging, or should be removed.
Symptoms Worth Paying Attention To
Most “holes” in the kidneys produce no symptoms at all. When they do, the signs tend to overlap regardless of the underlying cause: dull or sharp pain in the side or back, blood in the urine, recurrent urinary infections, or high blood pressure that’s hard to control. Fever alongside kidney pain suggests infection or abscess rather than a simple cyst. A sudden increase in pain could mean a cyst has ruptured or a stone has formed in one of the dilated collecting ducts.
If you’ve been told you have a cyst or “hole” on kidney imaging, the most important details are its size, its internal appearance, and whether it’s changing over time. A smooth, fluid-filled, thin-walled cyst found incidentally is almost certainly harmless. Anything with irregular walls, solid components, or rapid growth warrants closer evaluation.