The Overlooked Parasite-Autoimmune Connection and What It Means For You

In functional medicine, we’re always looking for the “why”. In most autoimmune cases, the answer is layered. There isn’t just one cause, but a combination of factors—because everything is connected. The mind, the body, the gut, the immune system, the brain, the endocrine system. Our genetics, our environment.  

The more we can put the puzzle pieces together, the more we can restore someone’s health and get them feeling well. And one piece that is often overlooked as a trigger or contributing factor to autoimmune disease is parasites. 

So today, we’ll take a look at the parasite-autoimmune connection, how to figure out if it applies to you, what to do next, and we’ll also take a look at how some parasites can actually be helpful for autoimmunity (I promise, it’ll make sense when you get there). 

Understanding Parasites: An Overview 

Parasites are organisms that live in or on another organism (a host) in order to survive. They can be classified into three main categories: 

• Protozoa: These are microscopic, single-celled organisms that reproduce inside your body. Examples include giardia, blastocystis hominis, and entamoeba histolytica. 
• Helminths: Helminths are parasitic worms like tapeworms, roundworms, hookworms, and ringworms that can live in your gut. 
• Ectoparasites: These are external parasites such as ticks or lice, which can also carry immune-disrupting pathogens. 

Misconceptions About Parasites

Parasites naturally conjure up a certain kind of image, and there are a lot of misconceptions around how they really affect us. 

First, parasites are common. Way more common than most people realize. Which brings me to the next important point: not all parasites cause harm for all hosts. For example, I see this a lot with blastocystis hominis: it shows up all the time on stool tests, but it often doesn’t cause symptoms. 

Both the parasite and the individual will determine whether a parasitic infection is problematic. Some parasites tend to cause more symptoms than others, but some individuals are also more susceptible (especially during certain periods of time, like if the gut is already compromised because of antibiotic use or stress). 

If a parasite isn’t correlated with your symptoms, you don’t usually need to worry about it. It can actually be a red herring. 

Something else that might surprise you: while you may be thinking mostly of the helminth category of parasites (worms) while reading this, the ones I most commonly see affecting my patients, by far, are microscopic protozoa. 

The Parasite and Autoimmune Connection

Autoimmune conditions including lupus, rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease (IBD), Hashimoto’s, and Graves’ have been linked to parasites. (1) So what’s the connection? 

There are several different ways that parasites can trigger autoimmunity. (2) Of course this doesn’t mean that parasites are always the cause of an autoimmune condition, but in some cases they’re a big piece of the puzzle. Here are a few different ways that parasites and autoimmune disorders may be connected: 

Molecular Mimicry

Molecular mimicry occurs when parasite proteins closely resemble your body’s own proteins. When the immune system attacks the parasite, it may mistakenly begin attacking the body’s own tissues too. 

Chronic Immune Activation

Pathogenic parasites can create low-grade, ongoing inflammation that pushes your immune system into a state of hyper-vigilance, throwing off the delicate balance between tolerance and reactivity. (3) 

Leaky Gut (Intestinal Permeability) 

Some parasites can damage the gut lining, allowing food particles, bacterial metabolites, and toxins into the bloodstream, triggering systemic inflammation and autoimmunity via the gut-immune axis.

It’s also worth noting that if your bio-terrain was already disrupted, you may have an increased susceptibility to both parasites and autoimmunity. For example, while parasites can damage the gut lining, an existing leaky gut is also a risk factor for parasitic infections. 

When parasites are in the mix, we always want to think about what has made your system a hospitable environment for a parasitic overgrowth, and address that environment (which we’ll get to a bit further down). 

Testing For Parasites

If you suspect that you may have a parasite issue behind your autoimmunity, the next step is to do some testing to try to find out. 

I would highly recommend working with a knowledgeable, ideally functional medicine practitioner who can help you select the right testing methods, interpret your results, and come up with a plan. There are so many nuances to parasites and parasite testing options, and a functional medicine practitioner will know what to focus on. 

These are some of the tests I do in my telehealth functional medicine practice, depending on the case. The reason I recommend a few different tests here is because I want to determine not just whether there’s a parasite present but how it may be affecting the body, and how the body is responding to it. 

Comprehensive Stool Testing

Stool testing is usually the starting point when it comes to detecting parasites. Conventional ova & parasite tests will screen for a handful of common parasites. I like to run a comprehensive gut microbiome stool test that looks at more kinds of parasites as well as fungal overgrowths, dysbiosis, and inflammatory markers. 

A multi-day stool collection is often a good idea, as many parasites don’t shed consistently and can be missed with a one-day sample.

Blood Tests For Parasite Antibodies

These tests can detect immune responses to specific parasites. Blood tests can measure IgG and IgM antibodies against common protozoa and helminths, and are helpful if the infection is outside of the gut. They can also point to past exposures (not necessarily an active infection) that still may have triggered autoimmunity. 

Organic Acid Testing

This is a specialized urine test that looks at metabolic byproducts excreted in the urine, including compounds associated with parasite and yeast overgrowth. It can give us clues about protozoan activity as well as things like fungal issues and detox pathway concerns. 

Depending on the individual case, I may also recommend different testing options to get a more complete picture (combined with your symptoms and history) of what’s going on. 

Holistic Treatment For Parasites 

There are several foods and medicinal herbs with very powerful anti-parasitic properties. If your practitioner does identify a symptomatic, chronic parasitic infection, here are a few holistic options to consider. 

Foods That Fight Parasites

Eating an anti-inflammatory, nutrient-dense diet is the first step when it comes to both treating parasitic infections and calming immune system dysregulation. 

From there, you can add in specific foods with anti-parasitic capabilities, including: 

• Garlic and onions (if you can tolerate FODMAPs) (4)
• Ginger (5)
• Pumpkin seeds (6) 
• Pomegranate 

Anti-Parasitic Herbs and Supportive Supplements

Herbal remedies can be incredibly powerful for fighting parasites. I recommend rotating protocols which may include any of the following herbs: 

• Black walnut (7)
• Wormwood (8) 
• Oregano oil (9)
• Grapefruit seed extract (10)
• Berberine 
• Otoba parvifolia
• Palo santo bark

Otoba parvifolia and palo santo bark are extracts from plants used in traditional South American medicine for centuries, and I’ve found them very effective with my patients. 

Other supplements that can help in a parasite protocol include probiotics, postbiotics, binders, and herbs that support the gut lining including marshmallow root or slippery elm. You can get my blend Gut Feelings here. 

It’s always best to get advice from a trusted practitioner before introducing any parasite treatments, especially if you’re planning to do a more comprehensive parasite cleanse. 

READ NEXT: How To Recognize and Treat Parasitic Infections 

Helminth Therapy: When Parasites Can Help Autoimmunity

Some parasites, specifically some kinds of helminths (worms), can actually be beneficial in autoimmune conditions. (11) 

This is the basis of helminth therapy, a treatment that’s still experimental but has shown promise through research for conditions including multiple sclerosis, Crohn’s disease, ulcerative colitis, and type 1 diabetes. (12) 

I know it sounds counterintuitive at first, but stay with me. Helminth therapy centers around the hygiene hypothesis or the “old friends” hypothesis, a theory behind the outsized prevalence of autoimmune and allergic diseases in industrialized countries. (13) 

The general idea is that we’ve overcorrected and oversanitized our environment, to the point that our immune systems don’t know how to regulate themselves. (14) Humans co-evolved with bacteria, fungi, and worms, which essentially trained our immune systems over time. In their absence, immune dysregulation and autoimmunity may become more common. 

Helminth therapy involves intentionally introducing non-human worms (such as pig whipworms) into the gut. These organisms likely don’t reach maturity in humans (and are therefore not thought to become infections). Instead, they may help: 

• Decrease pro-inflammatory cells including Th1 and Th17 (12) 
• Increase T-regulatory cells (15)
• Calm immune reactivity and gut inflammation
• Support microbiome diversity (16) 

I’ve had some autoimmune patients try helminth therapy (under supervision) and see great results. But just to be clear, it’s not a first-line therapy, and it shouldn’t be self-administered. This is a tool to consider for those who feel like they have tried everything else. 

A Personalized Approach to Autoimmunity

Knowledge is power when it comes to healing autoimmunity and chronic symptoms. The more we know about what’s causing or exacerbating the problem, the more targeted we can be when it comes to treatment approaches.  

If you’re looking for a personalized, root-cause focused approach to your autoimmune condition, or if you’re wondering about parasites that may be affecting you, please book a consultation with our telehealth functional medicine practice. 

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe.

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