How to Treat Intestinal Parasites Naturally

Finding out you’re harbouring a parasite in your GI tract can be a little scary. And whether it got there after food poisoning, overseas travel or drinking contaminated water, you want to get rid of it ASAP before it does anymore damage. If you’re not keen on antibiotics or have tried them unsuccessfully already, then let us show you how to treat intestinal parasites naturally.

Here is a summary of what we are going to cover:
> What are intestinal parasites and protozoa?
> Factors that increase your risk of getting a parasite
> What symptoms to look out for and why a parasite is often the cause of IBS
> The go-to parasite test we use with our clients
> How to treat parasites naturally and why antibiotics are not always a good choice

What are Intestinal Parasites and Protozoa?

A parasite is an organism that lives on or in a host organism (in this case, us!) and gets its food from or at the expense of its host. And while there are three main classes of parasites (shown in the diagram below), our focus is on protozoa parasites. These are the microscopic type of parasite that require lab tests to discover, including:
> Blastocystis hominis
> Dientamoeba fragilis
> Entamoeba histolytica
> Giardia lamblia / intestinalis
> Cryptosporidium parvum

While this isn’t an exhaustive list of protozoa parasites, they are by far the most common we see in our clinic and the ones we specialize in treating.

What are the risk factors for parasites?

It’s not always travel that leads to a parasite, but it is certainly one of the most common causes. Food poisoning from contaminated food and/or water, overly affectionate pets, poor hygiene practices, a hot and humid environment or an outbreak in your town’s water supply can all give you a nasty bug. You see, parasites are a normal part of life in every country on earth. It’s whether your immune system and microbiome are strong enough to fight it off that really matters.

It’s why we have stomach acid, good bacteria in our gut and an immune system to fight-off these ‘bad guys’. But, if you are stressed, intoxicated, fatigued, malnourished, have food sensitivities or any other illness or condition, your immune system is likely to be compromised, increasing your risk of a parasite with potentially lasting effects, like IBS.

Prior use of antibiotics also increases your risk of parasites. While antibiotics can sometimes be effective at killing a bacterial infection, they also destroy the good gut bacteria at the same time, creating an environment for opportunistic parasites to set up camp, proliferate and cause long-term chronic health conditions.

Common symptoms of a parasite infection

Parasites are major contributors to adrenal dysfunction, maldigestion, malabsorption, toxicity, detoxification issues, elimination and mucosal barrier problems within the body. They can contribute to fatigue, brain fog, depression and changes in hair, skin and nails. But most importantly, they can be the root cause of your IBS symptoms. Here are a couple of ways you can figure out if your IBS symptoms are being impacted by an intestinal parasite infection:

>  Cyclical diarrhoea - most parasites have specific life cycles and result in cyclical symptoms, such as diarrhoea. So, if you are doing okay for a week or two and then have an intense flare-up of symptoms for a few days and then do okay for another week or two and so on, that can be a real sign of a parasite.

>  Constipation - parasites can give off neurotoxins to ‘paralyse’ the muscles around the intestines, slowing peristalsis (intestinal movement) so that the organisms don’t get removed by the stool as easily as they may have before. Constipation can then create an environment in which parasites can further grow and proliferate.

>  Excess gas, bloating and abdominal cramps - these are all common symptoms reported by those suffering with intestinal protozoa.

>  Real food diet failures - if you have any IBS symptoms after you’ve tried any of the real food / low allergen diets like SCD, GAPS, Paleo or low-FODMAP diets for more than six weeks, then there is a high chance you have a parasite or other gut infection.

>  Secondary symptoms - like fatigue, hormone imbalances, weight gain, joint pain, nausea, headaches, foggy thinking, anxiety and depression could all be associated with a chronic intestinal parasite infection.

How to test for parasites

If you have any, or a combination of the above symptoms and risk factors, you’re probably wondering how to figure out what might be hiding in your gut. Here is the main test we use with our clients.

GI Map Stool Test / Complete Microbiome Mapping (PCR / DNA)

The GI Map by Diagnostic Solutions Laboratory (or Complete Microbiome Mapping as it is called in Australia), is the latest evolution of comprehensive DNA stool testing, using PCR technology. Before this testing was available locally in Australia, we would use a GI Map on many of our IBS clients whose symptoms remained despite a 'clean' CDSA stool test (see below) and we were amazed at the number of pathogens and elevated markers that showed up on the GI Map to further inform our healing approach.

There are three broad categories of markers that we look at on a GI Map to identify healing opportunities for IBS. These are pathogenic species, beneficial gut flora and intestinal health markers.
> Pathogenic species: whether these are identified in 'high' numbers or are simply 'detectable', pathogenic species are almost always something we need to address. These include parasites, worms, H. pylori, viruses, pathogenic and opportunistic bacteria, yeast/fungus.
> Beneficial gut flora: this section gives us clues about the overall abundance and diversity of your 'good' gut bacteria (microbiome).
> Intestinal health markers: these provide information about 'digestive fire', inflammation, your immune function and a helpful 'leaky gut' marker (zonulin).

GI MAP Test Result - Example Extract (USA)

GI Map Test Example.png

Complete Microbiome Mapping Test Result - Front Page Summary (Australia)

Complete Microbiome Mapping Test Example.png

Comprehensive Digestive Stool Analysis + PCR

A stool test is the oldest and most common form of testing for gut infections. While traditional techniques using visual (microscope) detection aren’t always reliable, the newer approach using DNA sampling (PCR) is much improved. This is why if you have had a stool test done by your GP in the past and it came back clean, this doesn’t mean there isn’t an infection. It might just mean the test you did didn’t detect it or wasn’t looking for the particular pathogen that you have. This is especially true if you had an MCS and not a PCR test.

Before the GI Map became widely available, the test we had our clients complete most often was a comprehensive assessment of the microbial environment of the gut. And while we prefer a GI Map these days, a good quality CDSA + PCR is still a good option if it’s the best you have available. It reports on pathogenic (parasites, bacteria and yeast/fungus) and imbalanced colonising organisms, as well as identifying the levels of beneficial flora. We like to test for pathogens beyond just parasites as most clients tend to have a mix of multiple pathogens in their gut causing their symptoms.

NutriPATH CDSA PCR Test Result - Example Extract

CDSA PCR Stool Lab Test Result

CDSA PCR Stool Lab Test Result

Here is a video on the testing process in case you are interested:

How do we eradicate an Intestinal Parasite?

Successfully eradicating a parasite infection requires a holistic approach focussed on dietary changes, lifestyle factors and targeted supplementation to address the root cause. This means we are going beyond just temporary symptom relief and supporting your body with healing your IBS and other symptoms that come with having a parasite. It also means that once the parasite and any other infections are removed and we have healed your gut from the damage caused, your body will be healthy and strong enough to fight off any attempted reinfection or other opportunistic pathogens in the future.

Because every client and every gut infection is so individual, it’s impossible to give really specific details in a blog post like this, but I’m keen to try to educate you on many of the considerations that go into developing a pathogen eradication protocol.

Treating parasites can be hard work. Not only are they often difficult to kill, the impact on the rest of your body during the process can be draining. Ever heard of “die-off”?  It’s a real thing and it sucks.  Basically, when the bugs die, they let off toxins that make us feel terrible. This is why it is really important to support your body, in the form of liver detoxing, rest, etc. while completing a pathogen eradication protocol. So here goes!

Parasite Treatment Protocol

When it comes to eradicating and healing from a parasite infection, we put our clients on a protocol that addresses diet, rest, exercise, stress reduction and supplementation. We specifically focus on the following:


Once we know what type of parasite you have, we can choose a diet that works for you. The primary food sources for most parasites are sugar and starch, so these must go. The Specific Carbohydrate Diet (SCD) or a Paleo-style Diet can be a good place to start.

The next thing we need to consider is removing any food sensitivities that can be contributing to inflammation in your GI tract and causing damage to your gut lining. These are identified by a food sensitivity test. Clients may find it easier to digest cooked, rather than raw foods at this time and we like them to include lots of anti-inflammatory omega-3 fats into their diet each day. Sources include: flax seeds and flax oil, chia seeds, walnuts and oily fish. Focus on organic products and aim for 2-3 litres of water (room temperature) or herbal tea to flush out toxins put out by the bugs as they die off.


Rest is an essential component of any healing protocol and often overlooked. Know this: if you don’t give your body the rest it needs to heal, you will not get better! Ideally, go to bed around 10pm and aim for 7-8 hours sleep each night. Good “sleep hygiene” means turning off those screens (phone, laptop and TV) and allowing 30 minutes to one hour before sleep each evening to wind-down by reading a book, journaling, meditating or listen to relaxing music. Trust me, this practice alone will change your quality of sleep if you commit.


Too much or too intense exercise for those with a parasite infection can put added stress on the body and do more harm than good. While it’s always important to move your body, a more gentle approach with exercise such as walking, yoga and restorative pilates will likely have the most positive impact on your healing. Once your gut is in better shape, you can return to all of the crazy-active things you love. Read more about exercise and gut issues in this post.

Stress Reduction

Removing and reducing stress on the body is a crucial part of any parasite eradication protocol.

This applies to all three categories of stress:

  • Mental/emotional: implementing relaxation and stress reduction activities such as meditation, journaling or Emotional Freedom Technique (EFT).

  • Physical: consider working with a chiropractor, acupuncturist, physio or other health professional to address any structural problems adding to your body’s overall stress.

  • Hidden/internal: these are things like hormone imbalances, liver issues, food sensitivities or leaky gut that we need to test for and eliminate to stop the constant inflammation in your body. A parasite itself is a hidden stressor and one that must go before you can return to full health.


Through our study, research and clinical practice, we have learnt that it is almost impossible to completely eradicate a parasite using diet alone. A pretty shocking truth and why we need to be smart and supplement, using natural botanicals - nature’s ultimate anti-pathogenic treatment.  

A few of our go-to supplements to support the body and heal from an intestinal parasite include:

First line of defence:

  • Natural antimicrobial herbal blends - These are the products that will kill off the parasites. We like products that contain multiple ingredients in a broad spectrum blend. Dosage is dependent on your health and the type/s of infection you have so we can’t go into detail about this here and we highly recommend consulting a practitioner before using these products.

  • A biofilm buster - Parasites and other gut bugs like to live and hide in the biofilm that are most commonly created by bacteria. Biofilms are colonies of microorganisms that are protected by an extracellular matrix – which we think of as a protective home for the infection to live in. For this reason, we need to break down biofilm to ensure we remove all of a parasitic infection.

  • Probiotics - These are essential to help build numbers of beneficial bacteria in the GI tract. Look for a product that contains at least 10-30 strains and 15-100 billion units to help bring in some good strains of bacteria and support the immune system and microbiome with fighting off all the bad bugs that are trying to take over. We like to use Primal Defense by Garden of Life for those who have parasites. Remember to always take probiotics away from natural antimicrobial herbal blends.

  • Digestive enzymes - We start our clients on digestive enzymes to support their digestion through the pathogen eradication process. Look for brands that contain protease (breaks down protein), amylase (breaks down carbs) and lipase (breaks down fats). A good product to start with is Digest by Enzymedica, however if you often see remnants of undigested food in your stool, you may need to use something a little more comprehensive like Digest Gold.

  • Liver Support - All of the toxins from the bugs are removed from the body via your liver. Once you start to kill them off this places a massive load on your liver. So it’s helpful to take liver support products to support detoxing. We like to use UltraLiv by BioMedica, Liver GI Detox by Pure Encapsulations or Liver Health by Gaia Herbs.

  • GI Detoxification - Often clients can experience a buildup of negative symptoms as they progress to full doses of their supplements. This is because the parasite is starting to die off and release toxins into the GI Tract. A really cheap and effective way to manage this toxin build up is to use activated charcoal. We most commonly use Activated Charcoal by Nature’s Way, or more comprehensive formulas such as G.I. Detox by Bio-Botanical Research.

Additional extras for support and healing:

  • Mucosal Barrier support - For individuals who have a leaky gut as a result of a parasite or other gut infection, it is essential to support healing of their gut lining at the same time as killing off the bad bugs. Again, we like to use a mucosal barrier support herbal blend for this, such as BioMatrix by BioMedica, GI Revive by Designs for Health or Comprehensive Gut Health by Pioneer Nutrition Formulas.

  • Constipation clear-out natural options - if you’re constipated, your body is storing toxins that will be making you feel terrible. These need to be cleared and daily bowel movements must happen before you begin to cause more toxic burden on your body as the bugs die off. If you want more information about how to clear constipation, please CLICK HERE to receive our FREE Constipation Clear-out guide.

“So, what about antibiotics?” you say. Well, that is a topic for a whole other blog post, but let’s just say that some antibiotics on their own can kill some parasite infections in the short term (weeks) but generally have poor relapse rates (because of the longer life cycles of some bugs and biofilms, amongst other things) and often cause so much damage to your good gut bacteria that your risk of chronic, autoimmune and other diseases increases significantly. Not always worth it when there are other options available.

Next steps…

So, there you go - everything (and more) you need to know about healing intestinal parasite infections and getting rid of IBS symptoms! If you suspect you have a parasite or other gut infection and you would like to get tested and have a personalised healing protocol developed specifically for you, please get in touch - we’d love to work with you!

Healing the gut is a journey. If you are ready to begin yours, please head to the Work With Us page to learn more about how we work online with clients in many countries to test for and treat the many root causes of IBS symptoms and other GI conditions.

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