The process of diagnosing Whipple disease typically includes the following tests:

  • Physical exam. Your doctor generally begins with a physical exam. He or she will look for signs and symptoms that suggest the presence of this condition. For example, your doctor may look for stomach tenderness and skin darkening, particularly on sun-exposed parts of your body.
  • Biopsy. An important step in diagnosing Whipple disease is taking a tissue sample (biopsy), usually from the lining of the small intestine. To do this, your doctor typically performs an upper endoscopy. The procedure uses a thin, flexible tube (scope) with a light and a camera attached that passes through your mouth, throat, windpipe and stomach to your small intestine. The scope allows your doctor to view your digestive passages and take tissue samples.

    During the procedure, doctors remove tissue samples from several sites in the small intestine. A doctor examines this tissue under a microscope in a lab. He or she looks for the presence of disease-causing bacteria and their sores (lesions), and specifically for Tropheryma whipplei bacteria. If these tissue samples don't confirm the diagnosis, your doctor might take a tissue sample from an enlarged lymph node or perform other tests.

    In some cases, your doctor may ask you to swallow a capsule that holds a small camera. The camera can take images of your digestive passages for your doctor to view.

    A DNA-based test known as polymerase chain reaction, which is available at some medical centers, can detect Tropheryma whipplei bacteria in biopsy specimens or spinal fluid samples.

  • Blood tests. Your doctor may also order blood tests, such as a complete blood count. Blood tests can detect certain conditions associated with Whipple disease, particularly anemia, which is a decline in the number of red blood cells, and low concentrations of albumin, a protein in your blood.


Treatment of Whipple disease is with antibiotics, either alone or in combination, which can destroy the bacteria causing the infection.

Treatment is long-term, generally lasting a year or two, with the aim of destroying the bacteria. But symptom relief generally comes much quicker, often within the first week or two. Most people with no brain or nervous system complications recover completely after a full course of antibiotics.

When choosing antibiotics, doctors often select those that wipe out infections in the small intestine and also cross a layer of tissue around your brain (the blood-brain barrier). This is done to eliminate bacteria that may have entered your brain and central nervous system.

Because of the lengthy use of antibiotics, your doctor will need to monitor your condition for development of resistance to the drugs. If you relapse during treatment, your doctor may change your antibiotics.

Treatment for standard cases

In most cases, Whipple disease therapy begins with two to four weeks of ceftriaxone or penicillin given through a vein in your arm. Following that initial therapy, you'll likely take an oral course of sulfamethoxazole-trimethoprim (Bactrim, Septra) for one to two years.

Possible side effects of ceftriaxone and sulfamethoxazole-trimethoprim include allergic reactions, mild diarrhea, or nausea and vomiting.

Other medications that have been suggested as an alternative in some cases include oral doxycycline (Vibramycin, Doryx, others) combined with the antimalarial drug hydroxychloroquine (Plaquenil), which you'll likely need to take for one to two years.

Possible side effects of doxycycline include loss of appetite, nausea, vomiting and sensitivity to sunlight. Hydroxychloroquine may cause loss of appetite, diarrhea, headache, stomach cramps and dizziness.

Symptom relief

Your symptoms should improve within one to two weeks of starting antibiotic treatment and go away entirely within about one month.

But even though symptoms improve quickly, further lab tests may reveal the presence of the bacteria for two or more years after you begin taking antibiotics. Follow-up testing will help your doctor determine when you can stop taking antibiotics. Regular monitoring can also detect development of resistance to a particular drug, often indicated by a lack of improvement in symptoms.

Even after successful treatment, Whipple disease can recur. Doctors usually advise regular checkups. If you've experienced a recurrence, you'll need to repeat antibiotic therapy.

Taking supplements

Because of the nutrient-absorption difficulties associated with Whipple disease, your doctor may recommend taking vitamin and mineral supplements to ensure adequate nutrition. Your body may require additional vitamin D, folic acid, calcium, iron and magnesium.

Clinical trials

Explore Mayo Clinic studies testing new treatments, interventions and tests as a means to prevent, detect, treat or manage this condition.

Preparing for your appointment

If you have signs and symptoms common to Whipple disease, make an appointment with your doctor. Whipple disease is rare, and the signs and symptoms can indicate other, more common disorders, so it can be hard to diagnose. As a result, it's often diagnosed in its later stages. However, an early diagnosis reduces the risk of serious health effects associated with not treating the condition.

If your doctor is uncertain about the diagnosis, he or she may refer you to a doctor who specializes in digestive diseases or to another specialist depending on the symptoms you're having.

Here's some information to help you get ready for your appointment, and know what to expect from your doctor.

Information to gather in advance

  • Write down your symptoms, including when you first noticed them and how they may have changed or worsened over time.
  • Write down your key medical information, including other conditions with which you've been diagnosed and the names of all medications, vitamins and supplements you're taking.
  • Write down key personal information, including any recent changes or stressors in your life. These factors can be connected to digestive signs and symptoms.
  • Take a family member or friend along, if possible. Someone who accompanies you may remember something that you missed or forgot.
  • Write down questions to ask your doctor. Creating your list of questions in advance can help you make the most of your time with your doctor.

For signs and symptoms common to Whipple disease, some basic questions to ask your doctor include:

  • What is the most likely cause of my condition?
  • Are there any other possible causes for my condition?
  • What diagnostic tests do I need?
  • What treatment approach do you recommend?
  • I have other medical conditions. How do I manage them together?
  • How soon do you expect my symptoms to improve with treatment?
  • For how long will I need to take medications?
  • Am I at risk of complications from this condition?
  • Am I at risk of a recurrence?
  • How often will you need to see me for monitoring?
  • Do I need to change my diet?
  • Should I take any nutritional supplements?
  • Are there any lifestyle changes I can make to help reduce or manage my symptoms?

Don't hesitate to ask any other questions you have.

What to expect from your doctor

A doctor who sees you for possible Whipple disease is likely to ask a number of questions, such as:

  • What are your symptoms, and when did you notice them?
  • Have your symptoms gotten worse over time?
  • Are your symptoms typically worse after a meal?
  • Have you lost weight without trying?
  • Do your joints hurt?
  • Do you feel weak or fatigued?
  • Do you have difficulty breathing or a cough?
  • Have you developed confusion or memory problems?
  • Have you noticed problems with your eyes or vision?
  • Has anyone close to you had similar signs or symptoms recently?
  • Have you been diagnosed with any other medical conditions, including food allergies?
  • Do you have any family history of bowel disorders or colon cancer?
  • What medications do you take, including prescription and over-the-counter medications, vitamins, herbs, and supplements?
  • Are you allergic to any medications?

Nov 08, 2022

  1. Apstein MD, et al. Whipple's disease. https://www.uptodate.com/contents/search. Accessed Nov. 13, 2020.
  2. AskMayoExpert. Whipple disease (adult). Mayo Clinic; 2019.
  3. Whipple disease. National Institute of Diabetes and Digestive and Kidney Diseases. https://www.niddk.nih.gov/health-information/digestive-diseases/whipple-disease. Accessed Nov. 12, 2020.
  4. Jameson JL, et al., eds. Whipple's disease. In: Harrison's Principles of Internal Medicine. 20th ed. McGraw Hill; 2018. https://accessmedicine.mhmedical.com. Accessed Nov. 13, 2020.
  5. Ferri FF. Whipple disease. In: Ferri's Clinical Advisor 2021. Elsevier; 2021. https://www.clinicalkey.com. Accessed Nov. 13, 2020.
  6. Imboden JB, et al. Whipple disease. In: Current Diagnosis and Treatment: Rheumatology. 3rd ed. McGraw Hill; 2013. https://accessmedicine.mhmedical.com. Accessed Nov. 13, 2020.


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