Why Does My Pilonidal Cyst Keep Coming Back?

Is it a recurrence, or a wound that never healed?

The first question is what actually happened. Three different things get called "my pilonidal cyst came back." A surgical wound that never fully closed. Disease that healed and then returned months or years later. Or an abscess that was drained for relief, with the sinus itself never removed. The first is a healing problem. The second is a true recurrence. The third is the original disease, still there. They are handled differently, and an examination usually tells them apart.

A wound that never healed is common enough to be a standard reason for a further operation. In a Danish hospital cohort of 380 patients having the cleft lift, every patient was operated on for one of three reasons: extensive disease, a wound that had not healed after earlier surgery, or a recurrence. Among the 79 adolescents in that cohort, 34 (43 percent) had the operation because an earlier wound never healed. In the original report on the cleft lift, 31 patients with the most stubborn disease had been through 141 operations between them and had lived with open wounds for a combined 252 years.

Studies also define "came back" differently, which is one reason published rates vary so much. If you have early disease that has not been operated on, our companion article Will a pilonidal cyst go away on its own? covers that question.

Why pilonidal disease comes back: the crease, moisture, and hair

Pilonidal disease is not a sign of being unclean. The best-studied explanation is mechanical. The crease between the buttocks is deep, warm, and moist, and the skin at the bottom of it is easily damaged. The surgeons who developed the cleft lift proposed in 2002 that the source of the disease is that skin, sitting in a moist cleft with little oxygen, rather than the deeper tissue, and that an operation which changes the shape of the cleft gives the skin a chance to heal. Removing infected tissue on its own leaves the crease exactly as it was.

Hair is the other half. A German study collected 624 hairs from inside the sinus cavities of 20 patients. Seventy-four percent had no root, the ends looked cut rather than broken, and the hairs were shorter than hair elsewhere on the same patients, about 0.9 centimeters on average. The authors concluded that these look like short cut hair fragments, for example from the head, that have worked their way into the skin, and they suggested that the source of those fragments needs to be dealt with to prevent the disease. That is their interpretation of what they saw. Hair growing near the cleft can matter too.

Family history plays a part as well. In a German cohort of 578 patients followed for decades, 68 (12 percent) had a parent or sibling with the disease, and their long-term recurrence rate was higher: 35 percent versus 22 percent at 15 years, and 52 percent versus 28 percent at 25 years. Body weight at the time of surgery was not associated with recurrence in that study.

Why a wound in the midline struggles to hold

A wound at the bottom of the crease is in a hard place to heal. It stays moist, it is pulled with every step and every time you sit, and hair collects in it. This is why where the scar sits matters as much as what is removed. In randomized trials, closing the wound off to one side of the crease has done better than a standard closure down the middle. A 2024 Cochrane review of 33 randomized trials with 3,667 participants, mostly young adults aged about 21 to 34, found that off-midline closure probably results in lower rates of recurrence (1.5 percent versus 6.8 percent; risk ratio 0.22, 95 percent confidence interval 0.11 to 0.45; 13 trials, 1,492 participants) and of wound infection (3.8 percent versus 11.7 percent) than conventional midline closure, and probably shortens healing by about five days. The reviewers rated that evidence as moderate certainty.

The same review found less of a difference against a newer kind of midline closure done without tension on the skin (recurrence 5.4 percent versus 7.8 percent, very low-certainty evidence), and little to no difference between the two best-known off-midline flaps, the Karydakis flap and the Limberg flap. Its authors wrote that the choice of procedure is likely to be based on a clinician's preference and experience, the patient's characteristics, and the patient's preferences.

Long follow-up tells the same story. In 583 patients from the German military followed for up to 20 years, recurrence after excision with the wound left open to heal was 8.3 percent at five years and 11.2 percent at ten, compared with 17.4 percent and 20.5 percent after midline closure. At 20 years it was 28 percent after open healing versus 44 percent after a midline closure that had healed without breaking open. These were mostly young men operated on decades ago. The point is the pattern: recurrence keeps rising for years after any operation, and midline closure rose most.

Recurrence by operation, and why follow-up time changes the numbers

The largest analysis of pilonidal surgery, published in 2018, reviewed 6,143 studies from 1833 to 2017 and pooled the results by operation and by how long patients were followed. Two related off-midline operations, the Karydakis flap and the Bascom cleft lift, were associated with recurrence of 0.2 percent (95 percent confidence interval 0.1 to 0.3) at 12 months and 0.6 percent (0.5 to 0.8) at 24 months, in an analysis of 89,583 patients across all operations and all study types. The Limberg and Dufourmentel flaps were associated with 0.6 percent (0.3 to 0.9) at 12 months and 1.8 percent (1.1 to 2.4) at 24 months in the randomized-trial analysis, which covered 11,730 patients across all operations. Primary midline closure showed long-term recurrence of up to 67.9 percent (53.3 to 82.4) at 240 months, which is twenty years out and a different pool of patients, so it cannot be set beside the two-year figures. The authors' conclusion was that recurrence depends on the operation and on follow-up time, and that both must be considered before judging any procedure.

Follow-up time matters because recurrences keep arriving. In 205 German patients interviewed a median of 14.8 years after their first pilonidal operation, 41 (20 percent) had a recurrence. Of those 41 recurrences, 29 (71 percent) appeared within four years; the median gap was 1.8 years and the longest was 16.5 years. The authors calculated that even a five-year follow-up still misses 25 percent of recurrences. So a study that follows patients for six months and a study that follows them for five years are measuring different things, and a low early number is not a lifetime promise for any operation, including the cleft lift.

Many first operations are reasonable choices

If you had an operation that did not hold, it does not follow that the wrong operation was chosen. Guidelines list several accepted ways to treat chronic pilonidal disease. The American Society of Colon and Rectal Surgeons' 2019 guideline says patients who need surgery may have excision with primary repair, with consideration given to closing off the midline, excision with the wound left open to heal, or excision with marsupialization, based on surgeon and patient preference. It says flap procedures may be performed, especially for complex and recurrent disease when other techniques have failed, and that endoscopic minimally invasive approaches may be used but require specialized equipment and expertise.

The German national guideline, updated in 2020, says there is no treatment that is simple, painless, quick to heal, and low in recurrence all at once, so treatment should be tailored to how the disease presents and how extensive it is. It describes wide excision with open healing as a safe procedure that heals slowly, says minimally invasive procedures such as pit picking may be used for small primary disease although their recurrence rate is higher than excision, and says off-midline procedures should be used for disease not suited to those. It also states that excision with midline closure is associated with poorer outcomes, and it no longer recommends that closure. That is the guideline's statement about an operation that was standard teaching for decades, not a judgment on any surgeon who performed it.

Cleft lift surgery: what it is and what the series show

The cleft lift, developed by John and Thomas Bascom, removes the diseased skin and pits, then draws intact skin across a flattened cleft so that the stitch line sits to one side, out in the open air rather than at the bottom of the crease. In their 2002 report, 31 patients with severe disease that had failed earlier surgery all healed, 28 after a single procedure and 22 within a week, with no recurrences over a median follow-up of 20 months in the 27 patients the authors could follow. That is the originators' own series, uncontrolled and in selected patients, which is why the two studies below matter more.

The largest single series is one surgeon's 700 consecutive patients treated between 1993 and 2020. Of those, 3.4 percent (confidence interval 2.1 to 4.8 percent) needed a revision operation, with failure defined as incomplete healing or recurrence requiring further surgery. The median follow-up for patients without recurrence was six months, and no late recurrences were seen among the 156 patients followed beyond 24 months. Revision was needed more often after previous failed surgery (5.3 percent) and when the wound reached the edge of the anus (15.5 percent). The author described the result as an overall success rate of 96.6 percent, by that definition and at that follow-up.

A Danish hospital cohort, independent of the operation's originators, followed its cleft-lift patients longer. Among 380 patients operated on for extensive, non-healing, or recurrent disease, with a median follow-up of 62 months, the five-year recurrence rate was 17 percent in adults and 19 percent in the 79 adolescents, a difference that was not statistically significant. The two studies measured different things over different lengths of time, so one cannot be subtracted from the other: one counts reoperations at a median of six months, the other counts recurrences at five years in a group with difficult disease. Both are published results, not results from this practice. The cleft lift is one of the operations we offer; our pilonidal cyst surgery page describes it in our own words.

Cleft lift recovery, and what the area looks like afterward

Published recovery figures come from individual series and vary with the technique and the patient. In one academic center's 141 consecutive patients having a modified cleft lift, the primary healing rate was 88 percent, the mean time to functional recovery was 13 days, the mean hospital stay was 1.2 days, and no recurrence was seen over a mean follow-up of 14 months. The most common problems were a fluid collection under the flap, partial separation of the wound, and a superficial infection. Those are the usual things that can slow a cleft-lift recovery, and in that series they did not change the outcome for most patients.

What the area looks like afterward is the point of the operation: a curved scar that sits off to one side of the midline, and a cleft that is shallower and flatter than before, so there is no deep moist groove for hair to collect in. We do not publish before-and-after photographs on this page. Recovery timelines, drains, dressings, sitting, work, and exercise differ between surgeons and between patients. Our service page describes recovery after the cleft lift in our own words. Whoever operates on you, follow that surgeon's instructions, and call them promptly for fever, spreading redness, worsening pain, or new swelling around a healing wound.

Hair control after surgery, and when a second opinion makes sense

Because cut hair fragments are part of the mechanism, hair control after surgery has been tested. In a randomized trial of 302 patients aged 11 to 21 at one children's hospital, adding laser hair removal to usual care lowered the share of patients with a recurrence at one year by 23.2 percentage points (95 percent confidence interval 13.1 to 33.2 points). The trial had a weakness: one-year follow-up was available for 63.6 percent of the laser group and 88.7 percent of the usual-care group, so the result is less certain than the numbers suggest, and it was in teenagers and young adults. A 2018 review of 14 mostly observational studies found recurrence of 9.3 percent (34 of 366 patients) after laser hair removal, 23.4 percent (36 of 154) after razor or cream removal, and 19.7 percent (85 of 431) with no hair removal. Shaving was not shown to help in that review.

The ASCRS guideline says hair removal from the cleft, by shaving or by laser, may be used as a primary or added measure. Whether, how, and when to remove hair near a healing wound is a question for the surgeon who treated you.

A second opinion is reasonable after one or more operations that did not hold, or when a wound has stayed open for months. Surgeons differ in which operations they perform, and an opinion from a surgeon who regularly performs off-midline procedures, such as the cleft lift, the Karydakis flap, or the Limberg flap, gives you a view of those options. Bring any operative or pathology records you have. The first operation was often a reasonable choice; asking is not an accusation.