Cysts form in the body through a handful of core mechanisms: blocked ducts, trapped skin cells, hormonal shifts, joint damage, genetic mutations, infections, and chronic inflammation. Most cysts are harmless, fluid-filled sacs that develop slowly and never cause symptoms. But the specific trigger depends entirely on where the cyst appears and what type of tissue is involved.
Blocked Ducts and Trapped Skin Cells
The most familiar cysts, the firm lumps that appear just under the skin, form when cells get pushed where they don’t belong. Despite often being called “sebaceous cysts,” most of these bumps are actually epidermal inclusion cysts. They aren’t filled with the oily substance your skin produces. Instead, they fill with keratin, a structural protein your body uses to build skin, hair, and nails.
The process starts when skin cells from the outer layer get forced into the deeper layer, typically from a small injury, a scratch, a surgical wound, or even a clogged hair follicle. Once those cells are trapped below the surface, they form a pocket that steadily fills with keratin and cellular debris. The pocket grows slowly over weeks or months into a round, firm lump you can feel rolling under your fingers. These cysts are not contagious and rarely dangerous, but they can become inflamed or infected if bacteria find their way in.
True sebaceous cysts, filled with the oily substance from oil glands, are actually uncommon. They’re mainly associated with a specific skin condition called steatocystoma multiplex, which causes clusters of small oil-filled cysts.
Hormonal Changes and the Menstrual Cycle
Ovarian cysts are among the most common cysts in women of reproductive age, and most are directly tied to the normal ovulation cycle. Each month, an egg develops inside a small fluid-filled structure called a follicle. The follicle is supposed to burst open, release the egg, then shrink. When that process stalls, either because the follicle never releases the egg or because it doesn’t drain its fluid afterward, the follicle swells into a cyst. These “functional” cysts are usually painless, resolve on their own within a few menstrual cycles, and rarely need treatment.
Hormonal imbalances can make this process go wrong more frequently. In polycystic ovary syndrome (PCOS), altered hormone levels prevent follicles from maturing to the point of ovulation. The result is many small, undeveloped follicles sitting on the ovaries, visible on ultrasound as a characteristic “string of pearls” pattern. PCOS affects an estimated 1 in 10 women of childbearing age and is driven by higher-than-normal levels of androgens, which disrupt the signaling that triggers egg release.
Joint Damage and Fluid Leaks
Ganglion cysts, the rubbery bumps that commonly appear on the wrist or top of the foot, form when the tissue covering a joint or tendon develops a small tear. Thick, jelly-like fluid from inside the joint leaks through the tear and collects in a sac just beneath the skin. Repetitive motion or a prior injury to the area can set the stage, though many ganglion cysts appear without any obvious cause. They can fluctuate in size, sometimes shrinking when you rest the joint and swelling when you use it heavily.
A Baker cyst (also called a popliteal cyst) follows a similar principle but forms behind the knee. The underlying trigger is almost always a problem inside the knee joint itself. Osteoarthritis, rheumatoid arthritis, or a torn cartilage (meniscus tear) causes the knee to produce excess fluid. That fluid gets pushed into a pouch at the back of the knee, creating a visible bulge that can feel tight or uncomfortable when you bend or fully straighten your leg. Treating the underlying knee problem is typically the key to resolving the cyst.
Genetic Mutations
Some cystic diseases are written into a person’s DNA. Polycystic kidney disease (PKD) is the clearest example. Mutations in specific genes cause fluid-filled cysts to grow throughout the kidneys, sometimes numbering in the hundreds and gradually replacing healthy tissue.
The most common form, autosomal dominant PKD, requires only one copy of the mutated gene to cause disease. About 90% of people with this form inherited it from an affected parent, while the remaining 10% developed a new mutation with no family history. A rarer form, autosomal recessive PKD, requires two copies of a different mutated gene (one from each parent) and typically appears in infancy or childhood.
At the cellular level, the mutations disable proteins that normally help kidney cells sense and regulate their own growth. Once those proteins stop working properly, cells begin proliferating abnormally, fluid accumulates, and cysts expand. The immune system compounds the problem: damaged cells release molecular signals that trigger inflammation, which in turn accelerates cyst growth. PKD affects roughly 1 in every 400 to 1,000 people and is one of the most common inherited diseases worldwide.
Aging and Simple Organ Cysts
Simple cysts in the kidneys and liver become increasingly common with age and are almost always discovered by accident during an imaging scan for something else. By age 50, roughly 40% of people have at least one simple kidney cyst. These are thin-walled, fluid-filled pockets that develop as kidney tissue changes over decades. They’re distinct from the genetic cysts of PKD because they’re few in number, don’t disrupt organ function, and don’t run in families. Liver cysts follow a similar pattern: benign, fluid-filled, and unlikely to cause any symptoms unless they grow unusually large.
Infections and Parasites
Certain infections cause cysts as part of the parasite’s life cycle. Cystic echinococcosis is one of the most significant examples worldwide. It’s caused by accidentally swallowing eggs from a tiny tapeworm called Echinococcus granulosus. Dogs are the primary carriers. They become infected by eating raw meat or organs from livestock, then shed tapeworm eggs in their stool. Humans pick up the eggs through direct contact with an infected dog’s fur, or by eating vegetables, drinking water, or touching soil contaminated with dog feces.
Once swallowed, the eggs hatch in the intestine and the larvae travel through the bloodstream to organs, most commonly the liver and lungs. There they slowly develop into large, fluid-filled cysts that can grow for years before causing symptoms. These parasitic cysts are structurally complex, with multiple internal layers, and can reach the size of a grapefruit or larger. They’re most common in rural farming communities where dogs have access to raw animal organs, particularly in parts of South America, Central Asia, the Mediterranean, and East Africa.
Inflammation and Chronic Disease
Chronic inflammation is a common thread behind many types of cysts. When tissue stays irritated or damaged over a long period, the body’s repair processes can go off course. Inflamed cells may wall off areas of damage, trapping fluid and debris inside a fibrous capsule. This is part of why conditions like rheumatoid arthritis lead to Baker cysts, why chronic acne can produce deep cystic nodules, and why inflammatory bowel conditions sometimes generate cysts in the abdominal cavity.
The immune system itself can worsen matters. In polycystic kidney disease, for instance, research has shown that the immune response may activate before the kidneys are visibly damaged. Injured cells release fragments of their own internal structures, which act as alarm signals that recruit waves of immune cells to the area. The resulting inflammation creates a feedback loop: cysts damage tissue, tissue damage activates immune cells, and immune activity promotes further cyst growth.
Cysts vs. Abscesses
Because cysts and abscesses can look similar from the outside, it helps to know the difference. A cyst is a closed sac, usually round and firm, that grows slowly and isn’t typically painful. It contains fluid, air, or semi-solid material like keratin. An abscess, by contrast, is a pocket of pus caused by a bacterial infection. It tends to appear quickly, feels warm and tender to the touch, and the surrounding skin is often red and swollen. The pus inside an abscess is a mixture of living and dead white blood cells, bacteria, and damaged tissue.
A cyst can sometimes become an abscess if it gets infected, which is why a lump that was stable for months and suddenly becomes painful and red may need prompt medical attention. An abscess almost always requires drainage and often antibiotics, while most cysts can be safely monitored. When cysts are removed, complete surgical removal of the sac lining produces better long-term results than simple drainage, which leaves the sac in place and allows it to refill over time.