If you have Crohn’s disease, you’re probably all too familiar with the gastrointestinal (GI) symptoms of a flare. But there are other, more surprising signs that inflammation is active, including symptoms that can affect your mouth, joints, and overall well-being.
General Symptoms of a Crohn’s Flare
There are general symptoms that “potentially indicate active Crohn’s disease,” says Joseph Feuerstein, MD, a gastroenterologist at the Center for Inflammatory Bowel Disease at Beth Israel Deaconess Medical Center and an associate professor of medicine at Harvard Medical School in Boston.
These include:
Diarrhea
GI bleeding
Bowel obstruction (symptoms include nausea, vomiting, not passing gas, and bloating)
It’s possible and common for people with Crohn’s to experience multiple symptoms at the same time. “It would be unusual, though, for any one of these symptoms on its own to be a sign of a Crohn’s flare,” says Dr. Feuerstein.
If you start to experience multiple symptoms, it may be time to see a doctor.
If you experience a loss of appetite and abdominal pain with nausea or vomiting, for example, Feuerstein says, it could be a sign of a stricture, which is a narrowing of the intestines caused by inflammation or scarring of the bowel walls.
A fistula, which is an abnormal connection or passage from the bowel into other tissues or organs, can lead to pus, blood, or stool leaking from the fistula opening on the skin, or through the organ the bowel is connected to, such as the vagina. If these symptoms are accompanied by fever, sweating or chills, quick, shallow breathing, or changes in your mental state, it can mean an infected fistula has become a life-threatening immune reaction called sepsis, which requires immediate medical attention.
Non-GI Signs of a Crohn’s Disease Flare
Up to 40 percent of people with an inflammatory bowel disease (IBD), including Crohn’s and ulcerative colitis, experience extraintestinal manifestations (EIMs): symptoms that occur outside the GI system. One study found that people with Crohn’s are more likely to have two or more EIMs than people with other forms of IBD. The causes of EIMs are unclear, says Feuerstein, but research suggests a genetic predisposition.
No matter the reason, EIMs can be a significant additional burden on those with IBD, and they can occur with inconsistent frequency depending on which organ is affected, before or after IBD is diagnosed. For those with Crohn’s disease, one research review found that the musculoskeletal system, skin, liver, gallbladder, bile ducts, and eyes were most likely to be affected.
The following are some common EIMs.
Arthritis
Inflammation of the joints is the most common EIM, affecting up to 30 percent of people with IBD. “Arthritis can affect the joints or the axial skeleton [the bones of the head and trunk],” Feuerstein says. Different types of arthritis may flare up along with disease activity or manifest independently of Crohn’s flares.
When arthritis develops with active disease, it typically gets better as intestinal symptoms improve. Chronic arthritis is more difficult to treat, says Feuerstein. “For immediate symptomatic relief, we always first recommend trying acetaminophen,” he says. People with IBD are typically told to avoid nonsteroidal anti-inflammatory drugs, or NSAIDs, due to the possibility of digestive upset. Biologic medications may be recommended for severe arthritis.
Skin Changes
Skin conditions can also be a complication of Crohn’s. Erythema nodosum is an EIM that causes raised, tender red bumps that usually appear on the shins and can affect up to 15 percent of people with Crohn’s. Pyoderma gangrenosum starts as a small bump or bumps on the skin and evolves into a large ulcer or ulcers that can grow and merge together, with raised borders, most often on the legs, though they can occur anywhere.
Liver Problems
A common complication of Crohn’s is metabolic dysfunction-associated steatotic liver disease (MASLD), formerly called nonalcoholic fatty liver disease, which rarely causes symptoms. Treatment of MASLD in people with Crohn’s is usually focused on improving diet and increasing physical activity.
A serious liver complication of Crohn’s is primary sclerosing cholangitis, which causes inflammation, scarring, and narrowing of the bile ducts. “While this is more common among people with ulcerative colitis, it can develop with Crohn’s disease as well,” says Feuerstein. “Typically, it’s a progressive EIM and may develop into cirrhosis and cholangiocarcinoma [cancer of the bile ducts].”
Also, the risk for gallstones is higher in those with Crohn’s disease than in people without the condition, according to research.
Eye Disorders
Most of the eye complications associated with Crohn’s are both treatable and unlikely to cause vision loss; they affect about 10 percent of people with IBD.Episcleritis, a condition that causes irritation and inflammation on the white of the eye, often goes away when Crohn’s symptoms begin to improve with treatment. Uveitis causes inflammation and pain in the middle layer of the eye — as well as blurred vision and light sensitivity — and may come on gradually or suddenly.
“Early recognition and treatment of uveitis is important,” says Feuerstein. If left untreated, the condition can become a medical emergency that may cause loss of vision.
Mouth Sores
Oral ulcers (canker sores) are most likely to occur during a flare and tend to subside when Crohn’s is under control. “For symptomatic relief, patients often use a lidocaine-based mouthwash,” says Feuerstein. “The lidocaine provides some numbing to alleviate the pain.”
Kidney Stones
These occur most often in Crohn’s with small bowel inflammation and in those who’ve had multiple small-bowel resections, says Feuerstein. Kidney stones usually cause sharp pain in the sides, lower back, or belly, as well as nausea, vomiting, and blood in the urine.
The calcium oxalate stones common in Crohn’s can be prevented with a limited-oxalate diet and adequate calcium. Oxalate is a chemical found mostly in plant foods, including spinach, beans, and nuts. Feuerstein says it’s important to drink lots of fluids, especially those that contain electrolytes.
Treatments for kidney stones vary depending on the severity of the symptoms. You’ll need to see a doctor and may need to consult with a nephrologist or urologist.
The Takeaway
Up to 40 percent of people with inflammatory bowel disease experience symptoms outside the GI tract, known as extraintestinal manifestations (EIMs).
EIMs commonly occur in the musculoskeletal system, the skin, liver, eyes, and other organs.
With Crohn’s disease, signs your condition has worsened and has become a full-blown flare include diarrhea and gastrointestinal (GI) bleeding, among other GI symptoms, but there may also be symptoms in other parts of the body.
Everyday Health follows strict sourcing guidelines to ensure the accuracy of its content, outlined in our editorial policy. We use only trustworthy sources, including peer-reviewed studies, board-certified medical experts, patients with lived experience, and information from top institutions.
Sepsis: Symptoms & Causes. Mayo Clinic. February 10, 2023.
Alizadeh M et al. Factors Associated With Extraintestinal Manifestations of Inflammatory Bowel Disease in SPARC-IBD. Inflammatory Bowel Diseases. November 2024.
Faggiani I et al. Extraintestinal Manifestations in Inflammatory Bowel Disease: From Pathophysiology to Treatment. Biomedicines. August 13, 2024.
Rogler G et al. Extraintestinal Manifestations of Inflammatory Bowel Disease: Current Concepts, Treatment, and Implications for Disease Management. Gastroenterology. October 2021.
Di Cola I et al. Joint Manifestations in Inflammatory Bowel Diseases, “Red Flags” for the Early Recognition and Management of Related Arthropathies: A Narrative Review. Journal of Clinical Medicine. February 26, 2025.
Barkhodari A et al. Inflammatory Bowel Disease: Focus on Enteropathic Arthritis and Therapy. Rheumatology and Immunology Research. July 6, 2022.
Solitano V et al. Metabolic Dysfunction–Associated Steatotic Liver Disease in Inflammatory Bowel Disease: A Proposed Stepwise Approach. Clinical Gastroenterology and Hepatology. February 2024.
Primary Sclerosing Cholangitis. Cleveland Clinic. July 27, 2025.
Hamid AM et al. Primary Sclerosing Cholangitis Associated With Ulcerative Colitis Coexisting With Cholangiocarcinoma: A Case Report. Cureus. June 17, 2024.
Baig MMA et al. Prevalence of Gallstones in Ulcerative Colitis and Crohn’s Disease: A Systematic Review and Meta-Analysis. Cureus. June 20, 2022.
Godman H. 3 Common Mouth Problems and How to Cope With Them. Harvard Health Publishing. October 1, 2022.
Zhang H et al. Causal Effects of Inflammatory Bowel Diseases on the Risk of Kidney Stone Disease: A Two-Sample Bidirectional Mendelian Randomization. BMC Urology. October 12, 2023.
Ira Daniel Breite, MD, is a board-certified internist and gastroenterologist. He is an associate professor at the Icahn School of Medicine at Mount Sinai, where he also sees patients and helps run an ambulatory surgery center.
Dr. Breite divides his time between technical procedures, reading about new topics, and helping patients with some of their most intimate problems. He finds the deepest fulfillment in the long-term relationships he develops and is thrilled when a patient with irritable bowel syndrome or inflammatory bowel disease improves on the regimen he worked with them to create.
Breite went to Albert Einstein College of Medicine for medical school, followed by a residency at NYU and Bellevue Hospital and a gastroenterology fellowship at Memorial Sloan Kettering Cancer Center. Working in city hospitals helped him become resourceful and taught him how to interact with people from different backgrounds.
Jen Laskey is a writer, editor, and content strategist. She has worked on EverydayHealth.com in various capacities since its inception, and her writing has appeared in many major publications, including SAVEUR magazine, EatingWell magazine, NBC, TODAY, and Fodor's Travel guides. She has also served as the senior editorial director of Twill Health, leading editorial strategy and daily operations for Twill's health and mental health apps.
In addition to writing about health, mental health, and wellness, Laskey writes regularly about food, wine/spirits, travel, and the arts. She is the author of Jen’s Candy Jar: Artisanal Candy Recipes for Special Occasions and is the founding executive editor of the multi-award-winning wine & spirits online trade magazine SevenFifty Daily.
She holds bachelor’s and master’s degrees in writing from Bennington College and Columbia University.
