How Anal Fistula Surgery Works — A Patient’s Guide to the 4 Procedures

If you’ve been told you need anal fistula surgery, you probably have one big question: what actually happens during the operation? The answer depends on which procedure your surgeon recommends — and for anal fistulas, there are four main techniques in use worldwide. This guide explains each one in plain language, so you know what to expect before you walk into the operating theatre.

Why Anal Fistula Surgery Is Necessary

An anal fistula is a tunnel between the inside of the anal canal and the skin near the anus. It usually forms after an abscess (a pocket of infection) drains, leaving a permanent channel behind. The tract is lined with infected tissue, and as long as it remains open, it will keep producing discharge and flaring into new abscesses.

Antibiotics and creams may calm symptoms briefly, but they cannot close the tunnel. The only way to cure an anal fistula completely is to remove or close the tract surgically. Fortunately, modern fistula surgery is highly effective and, in experienced hands, preserves normal bowel control.

What Happens Before Surgery

Before deciding on a procedure, your surgeon needs to map the fistula — how it runs, how much sphincter muscle it crosses, and whether there are branches or hidden pockets of infection. This is done through:

• A clinical examination including a digital rectal exam
• A proctoscopy to look inside the anal canal
• An MRI Fistulogram for complex or recurrent cases — this is the most accurate way to see the full tract
• Sometimes an Examination Under Anaesthesia (EUA), where the surgeon maps the tract in the operating theatre under anaesthesia

This mapping is what determines which procedure is right for you. A simple low fistula needs a different approach from a complex high one.

Fistulotomy — How It Works

Fistulotomy is the oldest and most reliable procedure for simple anal fistulas. It’s used for low fistulas that don’t cross significant sphincter muscle.

Here’s what happens during a fistulotomy:

Under anaesthesia, the surgeon identifies both openings of the fistula — the internal opening inside the anal canal, and the external opening on the skin. A small probe is passed through the tract to confirm its course. The surgeon then cuts open the length of the tunnel, allowing it to heal and flatten from the inside out.

After the tract is opened, infected tissue is gently scraped away to leave a clean wound. The wound is left open — not stitched closed — so that it heals from the bottom upwards. Stitching the skin closed at this stage would simply trap infection again.

Fistulotomy is typically a day-care procedure lasting 30–45 minutes. The open wound heals gradually over 6–8 weeks with daily dressings and sitz baths.

Seton Placement — How It Works

A seton is a thin surgical thread or band looped through the fistula tract. It’s used for complex or actively infected fistulas where cutting the tract open immediately would be unsafe.

During the procedure, the surgeon passes a fine probe along the tract from the external opening to the internal opening, then threads a soft seton through the tunnel. The two ends of the seton are tied loosely outside, so the thread sits inside the tract like a loose loop. Used for complex or infected fistulas, a surgical thread or band is looped through the tract to hold it open, allowing continuous drainage of infection over several weeks.

This sounds simple, but it does two important jobs. First, it keeps the tract drained so pus cannot build up into a new abscess. Second, it allows the tract to mature into a healthy fibrous channel, which makes definitive surgery much safer later on.

In many patients with complex fistulas, the seton is left in place for several weeks before a second, definitive procedure is performed. In selected cases — for example patients with Crohn’s disease — a long-term seton may be the main treatment.

LIFT Procedure — How It Works

LIFT stands for Ligation of Intersphincteric Fistula Tract. It’s a sphincter-sparing technique used for transsphincteric fistulas — fistulas that cross meaningful sphincter muscle and where preserving continence is a priority.

Here is how LIFT works:

The surgeon makes a small incision in the groove between the internal and external sphincter muscles. Through this incision, the fistula tract is identified where it passes between the two sphincters. The surgeon accesses the tunnel between the sphincter muscles, seals both ends with sutures, and divides the tract.

Because no sphincter muscle is cut and the tract is closed on the inside, the source of ongoing infection is removed without affecting bowel control. The small incision between the sphincters heals quickly, and recovery is faster than with open fistulotomy.

LIFT is usually performed after a seton has been in place for several weeks, which gives the tract time to mature and improves success rates.

Advancement Flap — How It Works

The advancement flap is used for high or recurrent fistulas where neither fistulotomy nor LIFT is suitable. It’s a more involved procedure but offers an excellent option for complex anatomy.

During the procedure, the surgeon scrapes out the fistula tract and covers the internal opening with a healthy flap of tissue taken from inside the rectum. The flap — a layer of healthy rectal lining (mucosa and submucosa) — is carefully mobilised, pulled down, and sutured over the internal opening of the fistula.

This achieves two things at once: the infected tract is removed, and the internal opening is sealed with healthy tissue. Once the source of infection is closed off, the rest of the tract heals from the outside in. The sphincter muscle is not cut, so continence is preserved.

The advancement flap is particularly useful for recurrent fistulas where previous procedures have not succeeded, or for high fistulas where opening the tract would damage the sphincter.

How Your Surgeon Decides Which Procedure Is Right

Procedure selection is based on the anatomy of your fistula and the findings on imaging. The main factors are:

• How much sphincter muscle the tract crosses
• Whether the fistula is simple (one tract) or complex (branches, multiple openings)
• Whether there is active infection that needs draining first
• Whether you have had previous fistula surgery
• Whether you have inflammatory bowel disease such as Crohn’s

Often, complex fistulas are treated in stages — a seton first to control infection and mature the tract, then a definitive procedure such as LIFT or advancement flap weeks later. Staged treatment gives the best balance of cure and continence.

What Happens on Surgery Day

Most fistula procedures are day care or one-night stays. The typical sequence is:

• Admission a few hours before surgery after overnight fasting
• Pre-operative consultation with the anaesthetist
• Surgery under spinal or general anaesthesia, lasting 30–60 minutes for most procedures
• Recovery in the ward with a first dressing check
• Discharge the same day or the following morning with written instructions

You’ll be given clear guidance on wound care, sitz baths, diet, and follow-up before you leave hospital.

Frequently Asked Questions

Q. How long does anal fistula surgery take?

Most fistula procedures take 30–60 minutes. Complex or staged cases may take longer. The vast majority are day-care procedures or involve a single overnight stay.

Q. Is the surgery done under general anaesthesia?

Either spinal or general anaesthesia is used, depending on the procedure and patient factors. The anaesthetist will discuss the best option with you before surgery.

Q. Can I choose my procedure?

Procedure choice is driven by the anatomy of your fistula and what imaging shows. Your surgeon will explain why a particular procedure is recommended for you. The wrong procedure for the wrong fistula gives poor results, so this is a decision best made jointly with your specialist.

Q. How soon will I know if the surgery worked?

Most fistulas show clear signs of healing within a few weeks. Final assessment of cure is usually made at six months, since the majority of recurrences appear within that window.