Crohn's disease

What Crohn's disease is

Crohn's disease is one of the two main forms of inflammatory bowel disease. The immune system attacks the gut wall, and unlike ulcerative colitis it is not confined to the lining of the colon. Three features define it.

• It can occur anywhere. Mouth to anus, though the last part of the small bowel and the right side of the colon are the commonest sites.
• It skips. Inflamed segments sit between entirely normal ones, which is why a colonoscopy alone can miss disease further up.
• It is full thickness. The inflammation goes through the bowel wall rather than staying on the surface. That is what allows it to scar into a narrowing, or to burrow through into a neighbouring structure.

That third point governs everything else. It is the reason imaging of the small bowel is part of the work-up, the reason damage accumulates quietly, and the reason the modern approach is to control the inflammation properly and early rather than to escalate slowly after damage has already been done.

Where it occurs, and the three patterns it follows

Two things are recorded at diagnosis and both shape what happens next: where the disease is, and how it behaves.

Where

Disease confined to the last part of the small bowel, disease confined to the colon, disease involving both, and separately whether there is any involvement of the upper gut. Location predicts which symptoms dominate and which tests are useful. Small bowel disease is invisible to a colonoscopy beyond the last few centimetres, which is why imaging is not optional.

How it behaves

• Inflammatory. Inflammation without narrowing or fistula. The pattern most people start with.
• Stricturing. Repeated inflammation and healing scars the wall and narrows the channel, producing obstruction.
• Penetrating. Inflammation burrows through the wall, forming a tract into another loop of bowel, the bladder, the skin or a collection.

Behaviour tends to progress over years, from inflammatory towards stricturing or penetrating. Preventing that progression, rather than reacting to it, is the main argument for treating Crohn's disease properly from the start.

What it feels like

Symptoms depend on where the disease is, which is why Crohn's is missed more often than ulcerative colitis. Small bowel disease in particular can go years without the obvious bleeding that sends people to a doctor.

• Abdominal pain, often in the right lower abdomen and often worse after eating
• Diarrhoea, with or without blood
• Weight loss without trying
• Tiredness, frequently from iron deficiency
• Fevers and night sweats
• Mouth ulcers that keep returning
• Pain, swelling or discharge around the anus
• In children and teenagers, growth slowing or puberty arriving late

How the diagnosis is made

Crohn's disease needs more than a colonoscopy, because a colonoscopy sees the colon and only the last few centimetres of the small bowel. Diagnosis combines endoscopy, imaging, blood and stool tests, and the biopsy results.

Colonoscopy with biopsies

Examines the colon and enters the last part of the small bowel. Biopsies are taken from inflamed and normal-looking areas alike, since microscopic changes in a normal-looking segment are informative.

Imaging the small bowel

MR enterography is the usual choice. It shows the length and site of affected segments, picks up strictures and fistulas, and involves no radiation, which matters in a condition diagnosed young and imaged repeatedly over decades. CT is used when the question is urgent. Capsule endoscopy can find subtle small bowel disease but is avoided where a stricture is suspected, because the capsule can lodge.

Intestinal ultrasound

Increasingly used in clinic. No preparation, no radiation, done in the room, and it answers the question of whether a segment is actively inflamed quickly enough to change the plan during the consultation.

Blood and stool tests

Inflammatory markers, a full blood count, iron, B12 if the last part of the small bowel is involved, and faecal calprotectin. Stool cultures and a test for Clostridioides difficile are done to exclude infection, both at diagnosis and at each significant flare.

Your care pathway

Smoking, and why it is raised every single time

Smoking is the one factor in Crohn's disease that a person can change and that genuinely alters the course of the illness. It is not a lifestyle footnote.

Pooled studies of people who had already had surgery for Crohn's found that smokers had about twice the risk of the disease returning clinically and about two and a half times the risk of needing a further operation, compared with people who had never smoked.

The important half of that finding is the other half. In the same analysis, people who had stopped smoking were not significantly different from those who had never smoked. The risk is not banked; it comes back down.

Perianal Crohn's disease

Inflammation can produce abscesses and fistulas around the anus: tracks running from the bowel to the skin. It is common, it is distressing, and people frequently delay mentioning it, which is the worst thing that can happen to it.

Pooled population studies put the risk at about one in five within ten years of diagnosis, with roughly one in nine already having perianal disease at or before the point the Crohn's itself is diagnosed. Disease involving the colon, and the rectum in particular, carries the higher risk.

Management is always joint, between gastroenterology and colorectal surgery. The usual sequence is an MRI of the pelvis to map the tracks, drainage of any abscess and placement of a seton to keep the track open and prevent it sealing over infection, then medical treatment to close the fistula. Operating to close a fistula while the bowel above it is still inflamed does not work.

How it is treated

Medicines are described here by class rather than by brand, because the right choice depends on the pattern of disease, its location, other medical conditions, what has already been tried and what is available.

The central principle has changed over the last decade. Crohn's disease accumulates damage, so the aim is to gain control early in people whose disease is likely to behave aggressively, rather than stepping up slowly and only reacting once a stricture or fistula has formed. Features that argue for early effective treatment include young age at diagnosis, extensive small bowel involvement, deep ulcers, perianal disease and needing steroids at the outset.

Corticosteroids

Settle a flare and do nothing to keep it settled. They do not heal the bowel reliably and they do not prevent damage. A locally acting steroid is used for limited ileal disease. Needing repeated courses means the underlying treatment is not working.

Immunomodulators

Immune-modifying tablets or injections used to maintain remission, and often used alongside a biologic to make it work better and last longer. Thiopurines are the usual choice; a second class is used where those are not tolerated or not suitable. Both need regular blood monitoring, and neither works quickly enough to rescue an acute flare.

Advanced therapies

• Anti-TNF agents. The longest track record in Crohn's, and the best evidence in perianal fistulising disease.
• Anti-integrin agents. Largely gut-specific in their action.
• Anti-interleukin agents. Effective with a favourable safety profile, now a common choice.
• JAK inhibitors. Taken as tablets, with prescribing attention to cardiovascular and clot risk.

Where a biologic is used, drug levels and antibodies are measured when the response is lost, which distinguishes a dose that is too low from a drug the body has learned to clear. That distinction decides whether to adjust the dose or change class, and getting it wrong wastes a treatment option that cannot be got back.

In Australia, access runs through the Pharmaceutical Benefits Scheme, which sets criteria for starting and continuing each agent. That is part of the planning conversation rather than an afterthought.

Strictures and narrowing

A stricture is a narrowed segment. The practical question is always how much of the narrowing is active inflammation, which responds to medicine, and how much is scar tissue, which does not. MR enterography and ultrasound help answer it, and the answer decides the whole approach.

Short strictures that are mainly scar can often be stretched at endoscopy with a balloon, which avoids an operation and can be repeated. Longer or more complex strictures, and those with a fistula or abscess involved, are better served by surgery. Balloon dilatation of Crohn's strictures sets out what that procedure involves, who it suits and when surgery is the better option.

Surgery, and stopping it coming back

Surgery in Crohn's disease is different from surgery in ulcerative colitis. Because the disease can occur anywhere, removing an affected segment removes that segment, not the condition. Surgery is therefore planned to take as little bowel as possible and to be used at the right moment rather than as a last resort.

It is the right answer for a fixed stricture causing obstruction, for a fistula or abscess that will not settle, and sometimes for localised disease where an operation gives a better outcome than years of escalating medication.

The part that gets least attention and matters most is what happens afterwards. Crohn's disease tends to return at the join, and it returns on endoscopy long before it returns as symptoms. So the plan after an operation includes preventive medication for those at higher risk, and a colonoscopy at around six to twelve months to look at the join directly. Treatment is then adjusted on what is seen, not on how the person feels. Stopping smoking is the other half of that plan.

How it is monitored, and what treatment is aiming at

Symptoms and inflammation line up poorly in Crohn's disease. People feel well with ulcers present, and people feel unwell with a healed bowel because scarring or bile salt diarrhoea is causing the symptoms instead. Monitoring therefore uses objective measures alongside how you feel.

The targets come from the treat-to-target framework set out by the International Organization for the Study of IBD, in the consensus known as STRIDE, updated in October 2026 as STRIDE-III.

Three kinds of target

• Actionable. Backed by trials showing that treating towards them improves outcomes. Missing one, after the current treatment has been properly optimised, is a reason to change treatment.
• Adjunctive. Linked to better outcomes but without trial proof that chasing them helps. They prompt closer monitoring and fine-tuning rather than a change of drug class.
• Patient-centred. Quality of life, disability and fatigue, now formal targets in their own right, approached by shared decision rather than by rule.

The timeline

The calprotectin numbers changed

• Under 200 micrograms per gram is the acceptable range.
• Under 100 is the level associated with transmural remission.
• 100 to 200 is a grey zone, interpreted with everything else.
• Persistently over 200 after adequate time and optimisation means the target has not been met.
• Results are confirmed on repeat testing rather than acted on from a single value.

Calprotectin is highly sensitive to inflammation in the colon but less so for disease high in the small bowel, which is one reason imaging is not replaced by a stool test.

What is actually tracked

• Faecal calprotectin at intervals, not only when something feels wrong
• Inflammatory markers, full blood count, iron, B12 and vitamin D
• Intestinal ultrasound or MR enterography for the small bowel and the bowel wall
• Colonoscopy at planned points, including after surgery
• Drug levels where a biologic is being used and the response has changed
• Bone density where there has been significant steroid exposure
• Skin checks and vaccinations, which immune-modifying treatment makes more important

Nutrition and diet

Diet matters more in Crohn's disease than in ulcerative colitis, for two reasons: the small bowel is where nutrients are absorbed, and exclusive liquid nutrition is a genuine treatment in some circumstances, particularly in children, where it can induce remission as effectively as steroids without the side effects.

Beyond that, no particular diet has been shown to control the disease. What does need attention is deficiency. Disease or surgery involving the last part of the small bowel affects B12 and bile salt handling. Iron deficiency is common. Low vitamin D is common. During a stricture flare a lower fibre diet reduces the risk of obstruction, but that is a temporary measure rather than a way to live.

A dietitian familiar with inflammatory bowel disease is worth seeing, in particular to stop a diet narrowing year on year in the hope of controlling something that diet does not control.

Pregnancy and family

Most people with Crohn's disease have straightforward pregnancies. As with ulcerative colitis, the single biggest factor is being in remission at conception. Active disease at conception tends to stay active and carries the genuine risks.

Most IBD medicines continue through pregnancy. Stopping them causes far more harm than the medicines do. Previous perianal disease or abdominal surgery is relevant to how the baby is delivered, which is a discussion to have with both teams well before the due date rather than in the third trimester.

Getting the most out of the appointment

• Where the pain is, when it comes and whether eating makes it worse
• Weight now and weight a year ago
• Any perianal symptom, however minor it seems
• Previous colonoscopy, MRI and CT reports with dates
• Operations, including how much bowel was removed and when
• Every medicine tried, the dose, how long for and why it stopped
• Smoking status, answered honestly, because it changes the plan
• Whether pregnancy is being considered in the next year or two

Where Crohn's disease is managed in Sydney

A/Prof Viraj Kariyawasam is a consultant gastroenterologist and hepatologist whose practice is focused on inflammatory bowel disease, with a particular interest in stricturing disease. He consults at Norwest, Rouse Hill, Pennant Hills and Macquarie Park.

Colonoscopy and balloon dilatation of strictures are performed at Norwest Private Hospital, Macquarie University Hospital and Pennant Hills Day Surgery. Perianal disease is managed jointly with colorectal surgery. New diagnoses, significant flares and perianal symptoms are prioritised. A referral from your GP is needed for a consultation.