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Colorectal surgery

Anal fistula surgery: fistulotomy, seton and other options in the UK

An anal fistula is a small tunnel between the end of the bowel and the skin near the anus, and it rarely heals without surgery. Which operation is suitable depends on where the tunnel runs in relation to the anal sphincter muscles. This guide explains fistulotomy, seton techniques and other options, what recovery and seton care involve, and the risks of recurrence and incontinence.

Last checked: 2026-10-10

Key facts

At a glance.

  • Surgery is usually needed

    The NHS says anal fistulas usually require surgery as they rarely heal if left untreated, and that surgery is recommended in most cases.

  • Two main operations

    The NHS names fistulotomy, which cuts open the whole length of the fistula so it heals as a flat scar, and seton procedures, where a surgical thread is left in the fistula for several weeks before a further procedure.

  • Protecting the sphincter

    The aim of surgery, according to NHS Wales (adapted from the NHS), is to heal the fistula and avoid damaging the sphincter muscles, which could result in loss of bowel control.

  • It can come back

    The Northern Care Alliance leaflet says it is common for a fistula to come back despite surgery and not unusual for some patients to have repeated operations.

  • Often day surgery

    The NHS says many people do not need to stay in hospital overnight after surgery, although some may need to stay for a few days.

  • Risks to discuss

    The main risks listed are infection, recurrence of the fistula and bowel incontinence, which is a potential risk with most types of treatment although severe incontinence is rare.

Why surgery is needed

An anal fistula is a small tunnel that develops between the end of the bowel and the skin near the opening of the bottom. The NHS explains that it is usually caused by an infection near the anus, which results in a collection of pus (an abscess); when the pus drains away, it can leave a small channel behind. Fistulas can cause discomfort and skin irritation, smelly discharge, and pus or blood on passing stool, and they do not usually get better on their own.

This is why surgery is the standard treatment. The Northern Care Alliance leaflet says that once a fistula is established an operation is often required to manage it, and that the aim is to drain any infection while avoiding damage to the sphincter muscles, the ring of muscles that open and close the anus and are responsible for continence.

Assessment before an operation

You will usually see a colorectal surgeon after a GP referral. The NHS lists a physical and rectal examination, a proctoscopy (a short telescope to look inside the anus) and an ultrasound, MRI or CT scan among the tests that may be used. The Northern Care Alliance says an MRI scan may be carried out to assess the fistula before surgery.

NHS Wales says that sometimes you may need an initial examination of the area under general anaesthetic to help determine the best treatment. The leaflet adds that some treatment decisions must be made while you are asleep during the operation, which is something to discuss with your surgeon beforehand.

The best operation depends on the position of the fistula and whether it is a single channel or branches in different directions. The NHS lists Crohn’s disease among the less common causes of fistulas, so your surgeon may ask about bowel symptoms.

The main operations

The table below summarises the options described by NHS Wales, adapted from the NHS website, and the Northern Care Alliance. Your surgeon will explain which are suitable for your fistula.

Surgical options for anal fistula
ProcedureWhat it involvesPoints from the sources
FistulotomyCutting along the whole fistula so it opens and heals as a flat scarThe most common operation and the most effective for many fistulas; usually only suitable if the fistula does not pass through much sphincter muscle
Loose setonA thread left in the tract for weeks to months so it drainsAllows drainage and prevents abscesses but does not cure the fistula
Cutting setonA tighter thread that slowly cuts through the tractMay need several procedures
Advancement flapFistula removed and the internal opening covered with a flap of rectal tissueConsidered when fistulotomy risks incontinence; lower success rate than fistulotomy but avoids cutting sphincter muscle
LIFT (ligation of intersphincteric fistula tract)Sphincter muscles moved apart and the tract sealed at both ends then cut openPromising results but only around for a few years, so more research is needed
Endoscopic ablationAn electrode passed through an endoscope seals the tractDescribed as working well with no serious safety concerns
Laser, fibrin glue, bioprosthetic plugSeals the tract without cutting muscleUncertainties about effectiveness; glue results may not be long-lasting

Living with a seton

A seton is a flexible thread passed along the fistula tract and tied loosely in a loop. The Northern Care Alliance explains that it allows the fistula to drain, prevents more abscesses forming and improves healing, and that you will continue to have a slight discharge. It says this is the safest option but does not cure the fistula, and that setons can stay in for weeks, months or years depending on the reason the fistula developed.

Seton care is mainly about keeping the area clean, allowing drainage and making sure the seton is not stuck. The leaflet suggests daily showers or warm salt baths, avoiding soap or perfumed products in the water until healed, regular dressing or gauze changes, and gentle daily flossing of the seton to prevent blockage. Once the initial wound has healed, it says a seton should be comfortable and should not affect bathing, swimming, sexual activity or bowel function, and that it is possible to live a full life with one.

It is understandable that learning that a seton may stay in for a long time can be stressful. The colorectal nursing team in a hospital is usually the best point of contact for advice, and your consultant’s team can explain the plan for the next stage.

Risks and recovery

NHS Wales lists the main risks as infection, which may need antibiotics and in severe cases hospital treatment; recurrence of the fistula despite surgery; and bowel incontinence, a potential risk with most types of treatment, although severe incontinence is rare and every effort is made to prevent it. The level of risk depends on the location of the fistula and the procedure.

The Northern Care Alliance explains that after a fistulotomy a small raw area heals with time, that sometimes a small dressing is needed but often the wound just needs to be kept clean with a small pad to prevent soiling, and that it is usually safe to cut a small amount of sphincter muscle, though you may notice a reduction in your ability to control wind at first, which should resolve with time.

Many people do not need to stay overnight, according to the NHS. Ask your surgical team about when you can return to work, driving and exercise, and what to do about pain, bleeding or a new abscess, because practice varies between units.

NHS route and private care in general terms

On the NHS, fistula surgery is arranged by colorectal surgeons after GP referral, often with a colorectal nurse specialist supporting seton care and dressings. Some people use private colorectal surgeons to be seen sooner, particularly for the initial assessment and scanning. Because fistula treatment may need several operations, it is sensible to ask who will be responsible for follow-up and for managing complications, and how repeat procedures would be arranged.

When to get help

See a GP if you have persistent symptoms of an anal fistula, according to the NHS. After surgery, contact your surgical team or NHS 111 if you have a high temperature, worsening pain, spreading redness or swelling, or heavy bleeding. The NHS lists a high temperature with swelling and redness around the anus as a sign of an abscess, which needs prompt assessment.

Frequently asked

Questions people ask.

Quick, plain-English answers to the questions we hear most.

  • Can an anal fistula heal without surgery?

    Rarely. The NHS says anal fistulas usually require surgery as they rarely heal if left untreated.

  • What is a fistulotomy?

    It is an operation that cuts open the whole length of the fistula so it heals into a flat scar. NHS Wales says it is the most common type of surgery and the most effective treatment for many fistulas.

  • What is a seton and why is it used?

    A seton is a surgical thread left in the fistula. It keeps the tract open to drain and heal without cutting the sphincter muscles. A loose seton drains but does not cure; a cutting seton gradually tightens.

  • Will I be incontinent afterwards?

    Bowel incontinence is a potential risk with most treatments, according to NHS Wales, although severe incontinence is rare. A small reduction in control of wind may occur at first after fistulotomy and should resolve.

  • Can the fistula come back?

    Yes. The Northern Care Alliance says it is common for a fistula to come back despite surgery, and it is not unusual to need repeated operations.

  • How long will I be in hospital?

    Many people do not need to stay overnight, according to the NHS, although some stay for a few days. Surgery is usually under general anaesthetic.

  • Why is an MRI scan done?

    The Northern Care Alliance says an MRI may be used before surgery to assess the fistula, particularly to show its path in relation to the sphincter muscles.

  • How long does a seton stay in?

    Weeks, months or even years depending on the reason the fistula developed, according to the Northern Care Alliance. The length of time is not always known in advance.

  • Is there a non-surgical option?

    NHS Wales says fibrin glue is currently the only non-surgical option, but it is generally less effective than fistulotomy for simple fistulas and results may not be long-lasting.

Where this comes from

Sources and checking.

This guide is for information, not medical advice.

Your GP or consultant knows your history and can tell you which parts apply to you. If your symptoms are severe, rapidly worsening, or come with red-flag features, seek urgent medical care. Figures and availability change, so treat them as a guide and confirm with the provider.

Published 2026-10-10, next review 2027-10-10.