Surgery & Complications
Crohn's disease is a transmural condition, meaning inflammation can penetrate all layers of the bowel wall and affect any part of the gastrointestinal tract. That depth of involvement is what makes the complication landscape broader and more structurally complex than many patients expect. About half of all Crohn's patients will develop a significant complication like a stricture or fistula within 20 years of diagnosis, and some will face complications outside the GI tract entirely. Understanding what can go wrong, how urgently it needs attention, and what monitoring looks like gives you a real advantage in catching problems early.
This guide organizes Crohn's complications by category, starting with the GI complications that are most common, then covering the extraintestinal manifestations that can affect joints, bones, eyes, liver, and more. Each section includes clear action thresholds so you know what warrants an emergency room visit versus a call to your gastroenterologist at the next available appointment.
Strictures: The Most Common Structural Complication
Strictures are narrowed sections of the intestine caused by repeated cycles of inflammation and scar tissue formation. They are among the most prevalent Crohn's complications. Roughly 25% of Crohn's patients develop at least one small bowel stricture, and 10% develop a colonic stricture. Looking further out, the lifetime risk of stricture formation is approximately 50%, and that number climbs to around 70% at the ten-year mark in some studies.
Strictures fall into two categories: inflammatory and fibrotic. Inflammatory strictures involve active swelling that narrows the intestinal passage and can often respond to medical therapy, including biologics and corticosteroids. Fibrotic strictures are composed primarily of scar tissue and typically do not respond to anti-inflammatory medication. Many strictures are a mix of both.
The symptoms of a developing stricture include cramping abdominal pain after eating, bloating, nausea, and a sensation that food is "getting stuck." These symptoms tend to worsen over time as the narrowing progresses. When a stricture becomes severe enough, it can lead to a bowel obstruction, which is the most common complication requiring hospitalization in Crohn's disease.
When to act: If you experience complete inability to pass gas or stool, progressive abdominal distension, and vomiting, go to the emergency room. A partial obstruction with intermittent cramping and reduced stool output warrants an urgent call to your gastroenterologist.
Bowel Obstruction: Recognizing the Emergency
Bowel obstruction occurs when a stricture or inflammation narrows the intestine enough to partially or fully block the passage of food and stool. Obstruction accounts for a significant proportion of Crohn's-related hospitalizations and together with fistulas and abscesses, stricturing complications account for 40-70% of surgeries in the first 10 years after diagnosis.
A partial obstruction may come and go, causing intermittent cramping, bloating, and reduced appetite. Patients sometimes learn to manage these episodes by switching to a low-residue diet during flares. A complete obstruction is a different situation entirely. It presents with severe, constant abdominal pain, inability to pass gas or stool, vomiting (sometimes of fecal material), and visible abdominal distension.
The treatment depends on the cause. If the obstruction is driven by active inflammation, IV corticosteroids and bowel rest may resolve it. If the obstruction is caused by fibrotic scar tissue, endoscopic balloon dilation or surgical resection may be necessary. The decision often requires imaging, typically a CT scan, to determine the nature and severity of the blockage.
When to act: A complete bowel obstruction is a medical emergency. If you cannot pass gas, are vomiting repeatedly, and have severe abdominal pain, go to the emergency room immediately.
Fistulas: Abnormal Connections Between Structures
Fistulas are abnormal tunnels that form between the intestine and other structures, including other loops of bowel, the bladder, the skin surface, or the vagina. They develop because Crohn's inflammation extends through the full thickness of the bowel wall. About 30% of Crohn's patients develop fistulas over the course of their disease.
The main types of internal fistulas in Crohn's disease include enteroenteral fistulas (bowel to bowel), enterovesical fistulas (bowel to bladder), and enterocutaneous fistulas (bowel to skin). Each type produces distinct symptoms. Enterovesical fistulas can cause recurrent urinary tract infections and pneumaturia (air in the urine). Enterocutaneous fistulas present as draining openings on the skin surface. Enteroenteral fistulas may cause diarrhea and malabsorption by allowing food to bypass sections of the intestine.
Perianal fistulas, which form around the anus, are common enough in Crohn's disease to warrant their own clinical discussion. They cause pain, drainage, and recurrent abscesses in the perianal area and often require a combination of medical therapy and surgical intervention.
Treatment for fistulas typically involves a combination of antibiotics, immunomodulators, and biologic therapy. Anti-TNF medications like infliximab have shown significant efficacy in fistula healing. When medical therapy is insufficient, surgical options include fistulotomy, seton placement, or in more complex cases, bowel resection.
When to act: Signs of an infected fistula or abscess, including fever, increasing pain, redness, and swelling, warrant same-day medical evaluation. Fecal drainage from the vagina or urine that smells like stool suggests an active fistula and requires prompt gastroenterology consultation.
Perforation: A Rare but Life-Threatening Emergency
Intestinal perforation occurs when chronic inflammation weakens the bowel wall enough that a hole develops. The contents of the intestine, which contain large numbers of bacteria, can spill into the abdominal cavity and cause peritonitis, a serious and potentially fatal infection. Perforation is rare in Crohn's disease compared to strictures and fistulas, but it is the most immediately dangerous complication.
Symptoms of perforation include sudden, severe abdominal pain that quickly becomes diffuse, a rigid or "board-like" abdomen, fever, rapid heart rate, and signs of shock such as lightheadedness and cold, clammy skin. The pain is typically constant and worsens with any movement.
When to act: Suspected perforation is a life-threatening emergency. Call 911 or go to the nearest emergency room immediately. Do not wait to see if symptoms improve.
Short Bowel Syndrome: A Post-Surgical Complication
Short bowel syndrome (SBS) develops when a significant length of small intestine has been surgically removed, often after repeated resections for strictures, fistulas, or abscesses. The remaining intestine cannot adequately absorb nutrients, fluids, and electrolytes from food.
SBS after extensive Crohn's resection can lead to chronic diarrhea, dehydration, weight loss, and nutritional deficiencies. The severity depends on how much intestine was removed, which segments were taken, and whether the ileocecal valve was preserved. Patients who have lost their ileocecal valve are also at higher risk for small intestinal bacterial overgrowth (SIBO), where bacteria from the colon migrate into the small intestine and interfere with digestion.
Management of SBS involves dietary modifications, oral rehydration solutions, and in some cases, parenteral nutrition (IV feeding). Medications that slow intestinal transit, like loperamide, can help reduce fluid losses. For patients with severe SBS, newer therapies like teduglutide (a GLP-2 analog) can promote intestinal adaptation and reduce dependence on parenteral nutrition.
When to act: Progressive weight loss, signs of dehydration (dark urine, dizziness on standing, dry mouth), or symptoms of specific nutrient deficiencies should be discussed with your gastroenterologist at your next appointment. Severe dehydration with inability to keep fluids down warrants urgent care.
SIBO: When Bacteria End Up in the Wrong Place
Small intestinal bacterial overgrowth occurs when excessive bacteria colonize the small intestine, where bacterial counts are normally low. In Crohn's disease, SIBO is particularly common after ileocecal resection, in the presence of strictures that create stagnant loops, or when fistulas connect different segments of bowel.
Symptoms of SIBO overlap significantly with Crohn's flare symptoms, making it easy to mistake one for the other. Bloating, gas, abdominal discomfort, and diarrhea are common in both conditions. SIBO can also cause fat malabsorption and vitamin B12 deficiency over time.
Diagnosis typically involves a hydrogen or methane breath test, though some gastroenterologists treat empirically with a course of antibiotics like rifaximin when SIBO is clinically suspected. The challenge with SIBO in Crohn's patients is that the underlying structural factors (strictures, surgical anatomy changes) often remain, making recurrence common.
When to act: If you notice new or worsening bloating, gas, and diarrhea that doesn't respond to your usual Crohn's management, bring it up with your gastroenterologist. SIBO is manageable but needs to be distinguished from a Crohn's flare because the treatments are different.
Kidney Stones and Gallstones: The Malabsorption Connection
Crohn's disease, particularly when it involves the ileum, disrupts the normal absorption of bile salts and fat. This disruption has downstream effects on both the gallbladder and the kidneys.
Crohn's patients have roughly twice the risk of developing gallstones compared to the general population. The mechanism involves bile salt malabsorption in the ileum, which changes the composition of bile and makes it more likely to form cholesterol-based stones. Patients who have undergone ileal resection are at even higher risk, and gallstones have been reported in 31-45% of patients with short bowel syndrome.
Kidney stones affect approximately 4.6% of Crohn's patients, with the most common type being calcium oxalate stones. When fat is poorly absorbed in the ileum, it binds to calcium in the gut, leaving oxalate free to be absorbed and excreted by the kidneys at higher concentrations. Male gender, active disease, prior intestinal surgery, and NSAID use are additional risk factors. Notably, having gallstones increases the risk of kidney stones nearly fivefold.
When to act: Gallstone symptoms (right upper abdominal pain after fatty meals, nausea) and kidney stone symptoms (severe flank pain, blood in urine) both warrant prompt medical evaluation. Discuss preventive strategies with your gastroenterologist if you have ileal disease or have had ileal resection.
Joint Complications: Arthritis in Crohn's Disease
Arthritis is the most common extraintestinal manifestation of Crohn's disease, affecting up to 30% of patients. Unlike typical osteoarthritis, IBD-related arthritis often strikes younger patients and can affect both large and small joints.
There are two main patterns. Peripheral arthritis affects the large joints of the arms and legs, including knees, ankles, elbows, and wrists. It tends to flare alongside intestinal disease activity, so treating the underlying Crohn's inflammation often improves joint symptoms. Axial arthritis affects the spine and sacroiliac joints, causing lower back pain and stiffness, particularly in the morning. Axial arthritis can follow an independent course from gut inflammation and may require separate treatment.
Treatment options include physical therapy, non-steroidal anti-inflammatory drugs (though NSAIDs can aggravate Crohn's symptoms), sulfasalazine for peripheral arthritis, and biologic therapies that target both gut and joint inflammation. Some biologics approved for Crohn's, such as infliximab and adalimumab, are also effective for inflammatory arthritis.
When to act: New joint pain, swelling, or morning stiffness lasting more than 30 minutes should be reported to your gastroenterologist, who may refer you to a rheumatologist. Joint symptoms that track with gut flares may improve as intestinal inflammation is controlled.
Bone Loss: Osteoporosis and Fracture Risk
Crohn's patients face an elevated risk of osteoporosis and bone fractures due to a combination of factors. Chronic inflammation itself interferes with bone metabolism. Corticosteroid use, a common treatment for Crohn's flares, accelerates bone loss. Malabsorption of calcium and vitamin D, especially in patients with ileal disease, further compounds the problem.
Bone density screening with a DEXA scan is recommended for Crohn's patients who have used corticosteroids for more than three cumulative months, have a history of low-trauma fractures, or have other risk factors for osteoporosis. Preventive measures include adequate calcium and vitamin D supplementation, weight-bearing exercise, and minimizing corticosteroid exposure by transitioning to steroid-sparing therapies when possible.
When to act: Ask your gastroenterologist about a DEXA scan if you have used steroids repeatedly or for extended periods. Unexplained bone pain or a fracture from minor trauma should prompt bone density evaluation.
Eye Complications: Uveitis and Episcleritis
Inflammation can affect the eyes in Crohn's disease, most commonly in the form of episcleritis (inflammation of the tissue covering the white of the eye) and uveitis (inflammation of the middle layer of the eye). Episcleritis causes redness and mild discomfort and typically resolves as intestinal inflammation is treated. Uveitis is more serious and can follow an independent course from IBD activity. It presents with eye pain, blurred vision, sensitivity to light, and redness, and can lead to permanent vision loss if untreated.
When to act: Eye pain, light sensitivity, or blurred vision require prompt evaluation by an ophthalmologist. Uveitis is treated with steroid eye drops and sometimes systemic immunosuppression. Do not assume eye symptoms are unrelated to your Crohn's disease.
Blood Clots: An Underrecognized Risk
Patients with Crohn's disease carry a two to threefold increased risk of venous thromboembolism (VTE), including deep vein thrombosis (DVT) and pulmonary embolism (PE). The risk is highest during active flares, with one large study finding a hazard ratio of 8.4 during flares compared to 2.1 during remission. Hospitalization, surgery, and corticosteroid use further amplify the risk.
In Crohn's disease specifically, the incidence of DVT is approximately 31.4 per 10,000 person-years, roughly 4.7 times the rate in the general population. The incidence of PE is approximately 10.3 per 10,000 person-years, about 2.9 times the general population rate.
Symptoms of DVT include swelling, pain, and warmth in one leg. PE symptoms include sudden shortness of breath, chest pain that worsens with breathing, rapid heart rate, and lightheadedness. Both conditions require immediate medical attention.
When to act: One-sided leg swelling with pain warrants same-day medical evaluation. Sudden shortness of breath or chest pain is a 911-level emergency. During hospitalizations or prolonged immobility, discuss VTE prophylaxis with your medical team.
Liver Complications: Primary Sclerosing Cholangitis
Primary sclerosing cholangitis (PSC) is a chronic liver condition that causes inflammation and scarring of the bile ducts. While PSC is more commonly associated with ulcerative colitis, it can also develop in Crohn's patients, with a prevalence of approximately 0.88%. Though relatively uncommon, PSC is a serious condition that can progress to cirrhosis and liver failure.
PSC often develops silently, with elevated liver enzymes on routine blood work being the first clue. As the disease progresses, symptoms may include fatigue, itching, jaundice (yellowing of the skin and eyes), and right upper abdominal discomfort. Patients with PSC also face an increased risk of cholangiocarcinoma (bile duct cancer) and colorectal cancer, requiring annual imaging and more frequent colonoscopies.
There is currently no medical therapy proven to halt PSC progression. Management focuses on treating symptoms, monitoring for complications, and evaluating for liver transplantation when the disease reaches advanced stages. An annual liver enzyme blood test is the standard screening approach for IBD patients.
When to act: Persistent fatigue, unexplained itching, or yellowing of the skin or eyes should be reported to your gastroenterologist promptly. Routine annual liver enzyme monitoring is recommended for all Crohn's patients.
Building Your Monitoring Baseline
The common thread across all Crohn's complications is that early detection makes a meaningful difference in outcomes. Strictures caught before they cause complete obstruction can be managed with endoscopic dilation rather than surgery. Fistulas identified early respond better to medical therapy. Nutritional deficiencies from malabsorption are correctable when caught before they cause bone loss or other damage.
Knowing your baseline, what your symptoms normally look like during remission, what your lab values typically are, and how your body responds to certain foods, gives you the ability to recognize when something has shifted. Keeping a consistent record of symptoms, flare patterns, and lab results creates the kind of longitudinal picture that helps both you and your medical team make better decisions.
Knowing your baseline helps you recognize complications early. Track your symptoms consistently with Aidy so you can spot changes that warrant urgent attention.