Baker’s Cysts, Knee Pain, Gut Microbiome, and Rheumatoid Arthritis

Knee pain! It’s a reality for many of us, particularly those with imbalanced gut bacteria, autoimmune reactions, (16) or resultant arthritic conditions such as Rheumatoid Arthritis. But what if that knee pain were caused by a different problem? One of the most common errors in diagnosis, whether it’s self-diagnosing or by an actual physician, is believing that the next symptom you experience is part of the already-known problem. If you have RA and you develop knee pain, is it from RA or a different problem?
Well, it could be either, or a combination of the two! In any case, though, it’s important to understand the differences, because it is always important to know what you should do and when to seek professional treatment and advice. Today we dive into this issue as it relates to the knee, looking at a
problem known as a Baker’s Cyst and complications it can cause. (1)

To understand what the possibilities are, it’s important to understand the knee itself and its relevant anatomy. The upper leg, or thigh, has one bone and the lower leg has two. The thigh bone is also known as the femur and is the largest bone in the body. The lower leg has a large bone known as the tibia or shin bone, and a smaller one called the fibula.

Between these bones there is cartilage, which is the slick, lubricated material at the end of each bone, forming the bearing surface. Cartilage is constantly being created by cells called chondrocytes and destroyed by wear and tear. The ratio between these two factors is determined by nutritional status and biomechanics. If your knee is poorly controlled, it may wear out faster than the cartilage growth can keep up with. (2) Between these cartilage surfaces, our knees have fluid-filled sacs
called bursa. These bursa further lower the friction or resistance of
the joint, increasing efficiency. When a bursa becomes inflamed, we
call that bursitis. This alone can be a cause of knee pain.

As the bursa is filled with fluid, sometimes the bursa can develop a bulge, somewhat like a hernia, due to increased wear and tear from arthritis, poor biomechanics, injury, inflammatory damage such as RA, or infections such as Lyme Disease. When the fluid herniation swells into the popliteal space, which is in the back of the knee, this is called a Baker’s Cyst. These cysts can cause a variety of problems, from pain to emergency situations that can be life-threatening. (3)

There are veins and arteries that pass through the knee region, and it is possible for a Baker’s cyst to compress a vein such as the popliteal vein. If that compression is sufficient to severely limit blood flow, it can result in thrombophlebitis, or a blood clot in the vein. This is also known as deep vein thrombosis, or DVT, and can be life-threatening as the leg will effectively lose its blood flow. Symptoms include swelling, warmth and redness of the leg, with progressively increasing pain. (4,5)

Sometimes a blood clot will dislodge and travel through the circulation, where it can block a blood vessel in the lungs and cause a pulmonary thromboembolism or PTE which is also life-threatening. Symptoms
include chest pain, trouble breathing, coughing/coughing up blood, fast heartbeat. These are often rapid onset problems. (5)

Baker’s cysts can be palpated as a mass that forms in the deep tissues of the back of the knee, although they often can be quite large before being noticed in this way. The cyst can also extend down into the calf muscles, mimicking a pulled or torn muscle. Of course, any palpable mass should also be evaluated to ensure that it isn’t a benign or malignant tumor! In addition, palpable masses in this region can also be cysts caused by bacterial infection, or aneurysms or veins or arteries that pass through the knee. (7) These issues can cause complications or be life-threatening as well. For this reason, it is critical to correctly identify these types of masses.

An MRI image is often used for this diagnosis as it allows the radiographer to distinguish what type of tissue is involved and what structures it originates from. (6, 14)

A Baker’s cyst is often caused by erosive joint damage, and Rheumatoid Arthritis is a condition that causes erosion of the joint. It makes sense therefore that a Baker’s cyst can be caused by RA. These cysts can become quite large, with one example being 95x26mm in size! (8) A popliteal (Baker’s) cyst can also be caused by Lyme Disease, though this is thought to happen more often with children or teenagers than adults. Diagnosis is by antibody testing of the fluid, though this type of problem is not thought to be very common. (9) Due to the erosive nature of joint autoimmunity, Baker’s cysts in RA can also rupture. (10) If this occurs, the fluid from the cyst will migrate downward into and between the muscles in the calf, causing swelling and compression. This can result in compression of the vasculature, cause a “pseudothrombophlebitis” with calf pain, swelling and redness (but no actual blood clot, hence the “pseudo” part of the name!).

11 Fluid migration and swelling can also cause a compartment syndrome, where the tissues of the calf region become excessively compressed as fluid swelling occurs inside a non-stretchy fascial compartment. This can be extremely painful and even necessitate an emergency surgery to decompress the fascia. (14, 15) Baker’s cysts can be treated a variety of ways.

Short term solutions include fluid drainage to remove the accumulated fluid, as well as home remedies such as ice, compression wraps, and reduced physical activity.

A corticosteroid injection can also help reduce the inflammation, though it doesn’t address the underlying cause of the problem. Range of motion and strengthening exercises afterward can help to improve knee function to lower the chances of future episodes. If there is joint damage, such as a chip of cartilage that is weakening the joint bursa, surgery may be helpful to remove the offending fragment. (12)

Kinesiology taping of the back of the knee is a recognized strategy to help the region reduce swelling and redistribute fluid. This type of treatment can be easily used at home, though in this location on the body it’s almost impossible to apply to yourself, so you may prefer to see someone trained in using kinesiology tape. The technique works by lifting and unsticking the layers of fascia over an area, facilitating fluid drainage and has become a staple of many amateur and professional athletes. (13) After the acute swelling and pain of a Baker’s cyst has resolved, it is important to address the underlying biomechanical causes. These can relate to foot biomechanics and equilibrium stability. Approaches that are applicable here include kinesiology taping the knee itself, with the goal of improving the feedback from the knee to the brain-and therefore improving the brain’s control of the knee. While research studies have been slow to address this therapy, it is easily tested by evaluating equilibrium with eyes open or even with eyes closed (taking precautions to not actually fall and get injured even more severely!).

This can also be evaluated standing and squatting on a Bosu ball. If the tape is providing benefit, equilibrium stability should be improved. This can be tested by putting one foot in front of the other, like on a tightrope, and seeing how easily the position is maintained before and after taping. Additionally, comfort and stability in a biomechanically-correct squat are also useful. It is also a good idea to review the importance of the gut microbiome in inflammation and autoimmune conditions.

Besides reading or re-reading The Symbiont Factor (17) there are a number of newer studies published that expand on the reality that our gut bacteria help to modulate and direct how our immune system works. A dysbiotic (ie, imbalanced) gut bacteria microbiome results in an imbalanced immune system. This can result in joint inflammation and pain, or even in an autoimmune condition developing. Managing that autoimmune condition is helped by also managing your gut bacteria. This can mean testing your microbiome to see what specifically is out of balance. We offer one of the best tests for this, Gut Zoomer 3.0 from Vibrant Wellness. If you’d like more information about how to get it done, just email me at or call 888-516-1533 and I can provide sample reports, costs, and procedures involved.

If you have questions, I offer a free first visit to discuss testing options:

Or scan this QR code:

In summary, if you develop knee pain and feel a mass on the back of your knee, please see your physician to make sure that it isn’t a pathology that should be addressed medically. If you have Rheumatoid Arthritis, or frequent joint pain for another cause, it is easy to mistakenly assume that the next joint pain you experience is caused by RA or “your usual pain”. This may or may not be true, and as outlined above sometimes RA or other joint inflammation can cause secondary problems such as a Baker’s cyst. If your knee pain turns out to be a Baker’s cyst, I hope that this guide can help you to improve and get back to living a great life!


2 thoughts on “Baker’s Cysts, Knee Pain, Gut Microbiome, and Rheumatoid Arthritis

  1. Great timing! Dealing with knee issues. Had a BC repaired last year. In last 2 months I can barely walk. They are talking total knee replacement. I found it interesting your reference to Lyme’s disease. I finally found a primary here who acknowledged Lymes in AR!! Thank you for sending out these emails! Jackie Basart

    Sent from my T-Mobile 5G Device
    Get Outlook for Android

  2. Hi Neurodoc,

    I have one knee as you describe with a Bakers cyst that’s always there but swells when injured…. been there for many years…. didn’t know what to call it.

    When its swollen too much it makes the knee feel unstable.

    I’ve continued to use it cautiously.

    Thanks for the info…

    On Mon, Jan 10, 2022, 1:56 PM The Symbiont Factor Blog wrote:

    > Dr. Richard Matthews posted: ” Knee pain! It’s a reality for many of us, > particularly those with imbalanced gut bacteria, autoimmune reactions, (16) > or resultant arthritic conditions such as Rheumatoid Arthritis. But what if > that knee pain were caused by a different problem? One o” >

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.