Crohn’s Disease

Understanding Crohn’s Disease Diagnosis

Diagnosing Crohn’s disease requires piecing together details from different sources — from blood tests that reveal certain biological markers, to imaging scans that visualize the gastrointestinal (GI) tract. Each step provides more clarity, helping your health care provider diagnose Crohn’s and rule out other diseases.

But diagnosing your Crohn’s is about more than just medical tests — it’s about understanding how the results fit into your health narrative. In this guide, we’ll explore these diagnostic tools not as isolated steps, but as parts of your diagnostic story. Knowledge of the condition and available treatments will help you make informed decisions about your health.

Understanding Crohn’s Disease Diagnosis

Diagnosing Crohn’s disease presents unique challenges due to the variability in its presentation and symptoms, which often overlap with other gastrointestinal disorders. Unlike diseases with more straightforward diagnostic criteria, Crohn’s can manifest differently in each person, making the diagnostic process quite dynamic. 

This also means diagnosis can take a long time. In fact, one study published in the Journal of Crohn’s and Colitis found that while almost half of the participants with Crohn’s had been referred to a gastroenterologist within a year of symptom onset, another quarter had experienced symptoms for more than 5 years before receiving a referral. Other studies have found that even longer delays in diagnosis are not uncommon, and diagnosis often does not occur until after significant complications have developed. (Source, Source)

The Role of Clinical Assessment and Medical History

A thorough clinical assessment and a comprehensive medical history form the cornerstone of Crohn’s diagnosis. This assessment includes evaluating your symptoms, family history of Crohn’s or other inflammatory bowel diseases (IBD), and a detailed account of gastrointestinal symptoms. 

The variability and nonspecific nature of symptoms make it challenging to exclude other conditions, such as ulcerative colitis or irritable bowel syndrome (IBS).

Symptoms Checklist: What Providers Look For

Health care providers look for a range of symptoms commonly associated with Crohn’s disease. 

Symptoms are highly variable and include stomach upset and cramps, diarrhea, abdominal pain, fever, blood in the stool, and more.

In 2015, the International Organization for the Study of Inflammatory Bowel Disease developed a list of 8 key indications health care providers should consider when differentiating Crohn’s disease from other GI disorders:

  1. abscesses or other lesions in the anal area that are not related to hemorrhoids
  2. having a first-degree relative with inflammatory bowel disease
  3. weight loss of at least 5% of normal body weight in the previous 3 months
  4. chronic abdominal pain for more than 3 months
  5. nocturnal diarrhea
  6. low grade fever in previous 3 months
  7. absence of abdominal pain in the 30 to 45 minutes following meals 
  8. lack of rectal urgency


These are only guidelines. Your symptoms may not align with the typical symptoms associated with Crohn’s disease and could be more ambiguous. Never ignore severe or ongoing changes to your health, no matter how vague or nonspecific they are. 

In addition to evaluation of symptoms, diagnosis of Crohn’s disease involves a combination of procedures and tests to confirm the presence of inflammation in the digestive tract, rule out other conditions with similar symptoms, and determine the extent and severity of the disease. 

The first diagnostics recommended will vary depending on your physical presentation, symptoms, medical history, and family history. 

Laboratory Tests for Crohn’s 

Laboratory tests help clinicians differentiate Crohn’s from other conditions. Lab test results provide key information and help rule out other diseases and conditions, including infections, and they’re often the first step recommended by a health care provider.

Complete Blood Count (CBC)

A complete blood count provides valuable insights into your red blood cells (RBCs), white blood cells (WBCs), and platelets, with each offering crucial information about the disease.

CBCs are useful for identifying Crohn’s markers, detecting anemia from blood loss in the GI tract, and helping rule out other potential causes of your symptoms, including infections. (Source)

Let’s break this down in more detail.

  • red blood cells and hemoglobin: RBCs and hemoglobin are vital indicators of anemia, a common complication in Crohn’s disease. Anemia in those with Crohn’s is often due to chronic intestinal bleeding or malabsorption of nutrients such as iron, vitamin B12, and folate. (Source)
  • white blood cells: An elevated WBC count is a marker of inflammation or infection. Inflammation is a key aspect of Crohn’s disease and monitoring WBCs can provide insights into the disease's activity and severity. A high WBC count might indicate an active disease state. (Source)
  • platelets: An increase in platelets often occurs in response to inflammation or bleeding. While not specific to Crohn’s, monitoring platelet levels can be a supplementary marker to gauge disease activity and guide therapeutic decisions. (Source)

Inflammatory Markers

Inflammatory markers, including the erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP), are clues that health care providers use to determine the extent of inflammation in the body. 

Since inflammation is a major component of Crohn’s, keeping an eye on these markers is key to both diagnosing and monitoring the disease.

  • erythrocyte sedimentation rate (ESR): This test measures how quickly erythrocytes (red blood cells) settle at the bottom of a test tube over a set period. Inflammation can cause these cells to clump together and settle more quickly, leading to a higher ESR. While a high ESR indicates increased inflammation, it’s not specific to Crohn’s disease and can be elevated in other conditions as well. (Source)
  • C-reactive protein (CRP): CRP is produced by your liver in response to inflammation. High levels of CRP are often found in active Crohn’s disease, but like ESR, elevated CRP is not exclusive to Crohn’s and can occur in other inflammatory conditions.  (Source)

Stool Tests

In Crohn’s disease, stool tests for calprotectin and lactoferrin help determine the source of intestinal discomfort and guide appropriate treatment. Recent studies have highlighted the growing importance of these biomarkers, and their reliability in clinical practice. The non-invasive nature of stool testing makes it a simple and effective option, reducing the need for more invasive procedures like colonoscopy when monitoring disease activity.


Calprotectin is a protein found in the white blood cells and is a reliable marker of inflammation in the GI tract. Elevated levels of calprotectin in the stool indicate intestinal inflammation, commonly associated with Crohn’s disease. It’s a sensitive and non-invasive biomarker, particularly useful in monitoring the disease's activity and response to treatment. 

The advantage of calprotectin lies in its helpfulness in differentiating between inflammatory bowel diseases and non-inflammatory conditions like irritable bowel syndrome. (Source)

In fact, 99% of people with IBD, including Crohn’s, have elevated fecal calprotectin levels. On the other hand, 15% to 20% of people with IBS have mildly elevated calprotectin levels. (Source)


Lactoferrin, another key protein present in the white blood cells, is also detectable in stool and mirrors intestinal inflammation. High levels of fecal lactoferrin point towards active inflammation, aligning with conditions such as Crohn’s disease. It is especially useful in identifying flare-ups or exacerbations of the disease. (Source)

Antibody Tests

Diagnosing Crohn's disease involves a detailed look at the immune system's responses. As with the CBC, these are blood tests, so they’re quick and easy to do. They’re primarily used to help distinguish Crohn’s from similar diseases, especially ulcerative colitis. (Source)

  • anti-Saccharomyces cerevisiae antibodies (ASCA): A positive ASCA result suggests an immune reaction to Saccharomyces cerevisiae, a common yeast. This reaction is more frequently associated with Crohn’s disease, making the ASCA test a valuable piece of the diagnostic puzzle for this condition. 
  • perinuclear neutrophil antibodies (pANCA): Because the pANCA test is more likely to be positive with ulcerative colitis, a negative ASCA result, especially combined with a positive ASCA, can lean the diagnosis towards Crohn’s disease. 

These lab tests are often combined both to diagnose and monitor Crohn’s, but they can’t replace imaging tests when it comes to a definitive diagnosis.


Endoscopy allows for direct observation and diagnosis of your gastrointestinal tract using a small camera, usually attached to a long tube. Endoscopy is considered the “gold standard” for diagnosing and observing Crohn’s and ruling out other conditions, such as cancer, ulcerative colitis, or diverticular disease. There are different kinds of endoscopy, depending on how the camera enters the body and which parts of the GI tract are visualized. (Source)

Colonoscopy: A Detailed Inspection of Your Lower GI Tract

A colonoscopy is a thorough examination of the colon (the large intestine) and the last part of the small intestine, known as the terminal ileum. It’s done using a colonoscope — a long, flexible tube equipped with a light and camera at the end — that is inserted through the anus.

What Health Care Providers Look For

During a colonoscopy, your provider is on the lookout for signs of Crohn’s disease that may include:

  • ulcers: open sores on the lining of your colon or terminal ileum
  • inflammation: redness, swelling, and signs of irritation along the intestinal lining
  • abnormal tissues: areas that don't look like your intestines’ healthy, smooth lining, which might indicate disease


The Role of Biopsies

During a colonoscopy the provider may perform a biopsy, in which small tissue samples are taken for evaluation under a microscope. The results of a biopsy may be helpful in predicting how Crohn’s will progress in the long-term and how severe it might become. This can be very helpful in planning a management course to minimize intestinal damage and optimize overall health. (Source)

Upper Endoscopy: Exploring Your Upper GI Tract

An upper endoscopy examines the esophagus, stomach, and duodenum (the beginning of the small intestine) using an endoscope, similar to a colonoscope but designed to navigate the upper GI tract. The upper GI tract is involved in around 16% of people with Crohn’s. (Source)

What Health Care Providers Look For

This procedure is particularly useful if you're experiencing symptoms related to the upper GI tract, such as difficulty swallowing or upper abdominal pain. The goal is to identify any signs of Crohn's disease in these areas, including ulcers, inflammation, or abnormal tissue patterns. (Source)

The Role of Biopsies

Just as in a colonoscopy, biopsies taken during an upper endoscopy are scrutinized for evidence of Crohn’s disease, offering a comprehensive view of how the disease may be affecting different parts of your GI tract.

Value of Endoscopy and Colonoscopy for Differential Diagnosis

Crohn’s disease and ulcerative colitis share many symptoms but affect your body in different ways and require different treatments. Here’s how upper endoscopy and colonoscopy help in distinguishing between the two:

  • location and extent of inflammation: Crohn’s disease can involve any part of the gastrointestinal tract and often affects it in patches, with healthy tissue in between. On the other hand, ulcerative colitis is limited to the colon and rectum and typically involves continuous stretches of inflammation. (Source)
  • depth of inflammation: During these procedures, your provider can observe whether the inflammation affects only the innermost lining of your intestine, as in ulcerative colitis, or affects multiple layers of the intestinal wall, which is characteristic of Crohn’s disease. (Source)

Capsule Endoscopy

A newer technique pioneered in the early- to mid-2000s, capsule endoscopy involves swallowing a small, vitamin-sized capsule equipped with its own camera and light source. 

As the capsule travels through your GI tract, it takes thousands of high-resolution images, offering detailed insights into the condition of your intestines. It’s often used when a colonoscopy is inconclusive. (Source)

Why It’s Used

Capsule endoscopy is particularly useful in evaluating the small intestine, an area where Crohn’s-related changes often occur but are less accessible with conventional endoscopy. It can help detect inflammation, ulcers, and other signs of Crohn’s disease, providing crucial information for diagnosis and management. One study found capsule endoscopy could successfully diagnose Crohn’s in 71% of cases. (Source, Source)

Capsule endoscopy might not be suitable for everyone, especially if there’s a known or suspected stricture (narrowing) in the intestine, as there’s a risk the capsule could become lodged.

CT and MRI Scans

Imaging tests are important tools that help diagnose and monitor Crohn’s disease, with computerized tomography (CT) and magnetic resonance imaging (MRI) being the two key imaging techniques used. Less commonly, you may also be recommended to undergo a barium series study. 

CT scans are sometimes chosen when an endoscopy could risk bowel perforation or when Crohn’s presents as an acute toxic illness or infection. (Source, Source)

Here’s a closer look at these diagnostic tools.

Computerized Tomography (CT) Enterography

CT enterography is a specialized imaging test designed to provide a detailed view of the small intestine, an area often affected by Crohn’s disease. It uses a contrast agent and X-rays taken from different angles to produce high-resolution images.

What It Reveals

CT enterography is particularly effective in identifying areas of inflammation, strictures (narrow sections of the intestine), and fistulas (abnormal connections between the intestine and other organs). It can also detect abscesses, which are pockets of infection. (Source)

Magnetic Resonance Imaging (MRI)

MRI provides high-resolution images without the use of X-ray radiation, making it a safer option for repeated use.

What It Reveals

MRI is adept at showing the condition of the bowel wall and surrounding tissues, including detecting inflammation, strictures, fistulas, and abscesses. (Source)

It’s particularly useful for its ability to visualize soft tissues and assess the extent of disease involvement.

Barium Series Study

An upper GI series called a barium series study is another imaging test used in Crohn’s disease. It involves drinking a chalky barium sulfate solution, which coats and fills the inner intestinal lining. Barium is an X-ray-absorbing contrast material that coats any ulcers, inflamed areas, abnormal connections between parts of the intestine, strictures, or other damage caused by Crohn’s disease. (Source)

Barium studies are less popular today than other imaging tests. But while many health care providers choose CT or MRI enterography, some gastroenterologists still use upper GI barium studies to evaluate the stomach and duodenum affected by Crohn’s. 

Genetic Testing

Genetic testing is another tool that helps guide personalized treatment for Crohn’s disease. A gene test is done using a blood or saliva sample. Specialist labs look to see if specific genetic changes related to Crohn’s risk are present. This may help confirm a diagnosis or determine how severe the disease may become.

For example, certain mutations, such as those found in the ATG16L1 and IL23R genes, have been associated with earlier onset and a more aggressive disease course, including the formation of strictures. (Source)

Knowing about particular gene variants can also guide treatment choices. For example, your genetics may suggest some medications will work better for you than others.

Understanding Differential Diagnosis For Crohn’s

Accurately diagnosing Crohn’s disease involves a thorough differential diagnosis, distinguishing it from conditions with overlapping symptoms such as ulcerative colitis, IBS, and celiac disease. 

Let’s delve deeper into how Crohn’s is differentiated from other similar gastrointestinal conditions:

Crohn’s Disease vs. Ulcerative Colitis

Both Crohn’s and ulcerative colitis are types of inflammatory bowel disease, with overlapping symptoms such as abdominal pain, diarrhea, and sometimes blood in the stool. (Source)

  • colonoscopy: A colonoscopy may reveal patchy inflammation and deeper ulcers characteristic of Crohn’s. In ulcerative colitis, the inflammation usually appears more continuous and limited to the innermost layer of the colon.
  • tissue analysis (histopathology): Analyzing tissue samples taken during a colonoscopy can further aid in differentiating Crohn’s from ulcerative colitis. In Crohn’s, these samples may show granulomas, which are small clusters of inflammatory cells, a feature not commonly seen in ulcerative colitis tissue samples. 

Crohn’s Disease vs. Irritable Bowel Syndrome

Though IBS and Crohn’s share symptoms such as abdominal pain and changes in bowel habits, there are significant differences between them. (Source)

  • IBS: This is a functional disorder, meaning it affects how the bowel works but doesn’t cause visible inflammation or tissue damage. It doesn’t appear on endoscopic exams or imaging tests the way Crohn’s does.
  • Crohn’s disease: This involves actual inflammation and damage to the bowel tissue, evident in endoscopic and imaging studies, and can lead to complications not seen in IBS.

Crohn’s Disease vs. Celiac Disease

While both can present with diarrhea and abdominal discomfort, they’re distinct in their triggers and the nature of the damage they cause. (Source, Source)

  • celiac disease: Triggered by exposure to gluten in susceptible individuals, celiac disease primarily damages the lining of the small intestine, leading to nutrient absorption issues. This damage is visible in tissue samples as villous atrophy (flattening of the small intestine’s lining).
  • diagnosis: Celiac disease can initially be identified through blood tests looking for specific antibodies, such as anti-tissue transglutaminase (tTG-IgA). Confirmation comes from examining small intestine tissue samples for signs of damage distinct from the patterns seen in Crohn’s.

Embracing Your Role in Your Health Care

Your knowledge of your body is invaluable. While medical tests might reveal inflammation levels or intestinal changes, your accounting of your own symptoms — such as abdominal pain, changes in bowel habits, or unexplained weight loss — adds depth to the overall diagnostic picture. Sharing your symptom experiences, no matter how minor they might seem, provides critical insights for diagnosis.

Your insights and lifestyle observations are indispensable in understanding and managing Crohn’s disease. Engaging in open dialogue with your health care team, documenting your experiences, and actively participating in your care process helps ensure you live your best possible life with Crohn’s. 

The Bottom Line

Crohn’s disease presents a diagnostic challenge due to its complex presentation and symptoms that overlap with other gastrointestinal conditions. There is no single test or procedure that will differentiate Crohn’s from other conditions that have similar symptoms, so reaching an accurate diagnosis involves some combination of patient history, lab tests, imaging studies, and procedures such as endoscopy and biopsy.

This painstaking process significantly improves the prognosis, allowing for timely management and treatment strategies that can slow disease progression and enhance quality of life.

Your active involvement in the diagnostic process is essential. By providing detailed accounts of your symptoms, lifestyle factors, and medical history, you can work with health care professionals to navigate the complexities of diagnosing Crohn’s disease in a collaborative approach that prioritizes patient engagement and empowerment.


Alula, K. M., & Theiss, A. L. (2023). Autophagy in Crohn’s disease: Converging on dysfunctional innate immunity. Cells, 12(13), 1779. 

Bjarnason, I. (2017). The use of fecal calprotectin in inflammatory bowel disease. Gastroenterology & Hepatology, 13(1), 53.

Bungay, H. (2011). Small bowel imaging in Crohn’s disease. Frontline Gastroenterology, 3(1), 39-46. 

Cappello, M., & Morreale, G. C. (2016). The role of laboratory tests in Crohn’s disease. Clinical Medicine Insights: Gastroenterology, 9. 

Crohn’s and Colitis Foundation. (n.d.). IBS vs IBD.

Danese, S., Fiorino, G., Mary, J.-Y., Lakatos, P. L., D’Haens, G., Moja, L., D’Hoore, A., Panes, J., Reinisch, W., Sandborn, W. J., Travis, S. P., Vermeire, S., Peyrin-Biroulet, L., & Colombel, J.-F. (2015). Development of red flags index for early referral of adults with symptoms and signs suggestive of Crohn’s disease: An IOIBD initiative. Journal of Crohn’s and Colitis, 9(8), 601–606.

Fiorino, G., & Danese, S. (2016). Diagnostic delay in Crohn’s disease: Time for red flags. Digestive Diseases and Sciences, 61, 3097–3098. 

Ghosh, S., & Mitchell, R. (2007). Impact of inflammatory bowel disease on quality of life: Results of the European Federation of Crohn's and Ulcerative Colitis Associations (EFCCA) patient survey. Journal of Crohn’s and Colitis, 1(1), 10–20.

Goran, L., Negreanu, A. M., Stemate, A., & Negreanu, L. (2018). Capsule endoscopy: Current status and role in Crohn’s disease. World Journal of Gastrointestinal Endoscopy, 10(9), 184.

Hendrickson, B. A., Gokhale, R., & Cho, J. H. (2002). Clinical aspects and pathophysiology of inflammatory bowel disease. Clinical Microbiology Reviews, 15(1), 79–94. 

Mayo Clinic. (2022, August 6). Crohn’s disease.

Naser, S. A., Arce, M., Khaja, A., Fernandez, M., Naser, N., Elwasila, S., & Thanigachalam, S. (2012). Role of ATG16L, NOD2 and IL23R in Crohn’s disease pathogenesis. World Journal of Gastroenterology, 18(5), 412.

National Institute of Diabetes and Digestive and Kidney Diseases. (n.d.). Symptoms & causes of Crohn’s disease. U.S. Department of Health and Human Services, National Institutes of Health.

Odeyinka, O., Alhashimi, R., Thoota, S., Ashok, T., Palyam, V., Azam, A. T., & Sange, I. (2022). The role of capsule endoscopy in Crohn’s disease: A review. Cureus, 14(7), e27242.

Pascual, V., Dieli-Crimi, R., López-Palacios, N., Bodas, A., Medrano, L. M., & Núñez, C. (2014). Inflammatory bowel disease and celiac disease: Overlaps and differences. World Journal of Gastroenterology, 20(17), 4846–4856.

Raman, S. P., Horton, K. M., & Fishman, E. K. (2013). Computed tomography of Crohn’s disease: The role of three dimensional technique. World Journal of Radiology, 5(5), 193. 

Rezazadeh Ardabili, A., Goudkade, D., Wintjens, D., Romberg-Camps, M., Winkens, B., Pierik, M., Grabsch, H. I., & Jonkers, D. (2021). Histopathological features in colonic biopsies at diagnosis predict long-term disease course in patients with Crohn’s disease. Journal of Crohn’s and Colitis, 15(11), 1885–1897.

Rubio-Tapia, A., Hill, I. D., Kelly, C. P., Calderwood, A. H., & Murray, J. A. (2013). American College of Gastroenterology clinical guideline: Diagnosis and management of celiac disease. American Journal of Gastroenterology, 108(5), 656. 

Sempere, G. J., Martinez Sanjuan, V., Medina Chulia, E., Benages, A., Tome Toyosato, A., Canelles, P., Bulto, A., Quiles, F., Puchades, I., Cuquerella, J., & Celma, J. (2005). MRI evaluation of inflammatory activity in Crohn’s disease. American Journal of Roentgenology, 184(6), 1829–1835. 

Spiceland, C. M., & Lodhia, N. (2018). Endoscopy in inflammatory bowel disease: Role in diagnosis, management, and treatment. World Journal of Gastroenterology, 24(35), 4014. 

Van Assche, G., Dignass, A., Panes, J., Beaugerie, L., Karagiannis, J., Allez, M., Ochsenkühn, T., Orchard, T., Rogler, G., Louis, E., & Kupcinskas, L. (2010). The second European evidence-based consensus on the diagnosis and management of Crohn’s disease: Definitions and diagnosis. Journal of Crohn’s and Colitis, 4(1), 7–27. 

Veauthier, B., & Hornecker, J. (2018). Crohn’s disease: Diagnosis and management. American Family Physician, 98(11), 661–669.

Vermeire, S., Van Assche, G., & Rutgeerts, P. (2006). Laboratory markers in IBD: Useful, magic, or unnecessary toys? Gut, 55(3), 426–431.