Stool tests are very useful when searching for root cause problems of the digestive tract. Stool testing is often ordered by functional medicine doctors because there is a tremendous amount of information these tests can provide. So what kind of information can you get from a stool test? 

They provide information about digestion, absorption, bacterial imbalance, yeast overgrowth, parasite infection, inflammation, metabolic activity and immune function. Let’s look at some of these in more detail and their importance.


This is the process of breaking food down into very small particles. Digestion relies heavily on proper levels of stomach acid and digestive enzymes from your pancreas.  Taking antacids or reduced production of stomach acid can interfere with your ability to break down food. Low stomach acid can also reduce absorption of nutrients like iron, calcium, zinc, B12 and magnesium. If you do not digest your food well, it is more difficult to absorb the nutrition from it. Undigested food also acts as a trigger for the immune system and leads to inflammation of the digestive tract. Your ability to digest food can be evaluated by a stool test.


This is the process of taking the broken-down food (digested food) and absorbing it into your body. This takes place in your small intestine. Poor absorption can be caused by poor digestion, leaky gut (small intestine) or the presence of too many bacteria in the small intestine; called SIBO (small intestinal bacterial overgrowth). If the health of the small intestine is compromised, you will not absorb the nutrients your body requires. Having large numbers of bacteria in the small intestine rob your body of nutrients because they get access to these nutrients before you are able to absorb them.  You might be eating a very healthy diet or taking dietary supplements, but if you are not absorbing these nutrients, they won’t do you any good.

Bacteria, Yeast and Parasites

A functional medicine stool test will test for the presence of different types of bacteria and yeast in the bowel. We often find that people taking probiotics still have low levels of beneficial bacteria and high levels of harmful bacteria or yeast. Harmful bacteria can compromise our body’s ability to detoxify  and can even change the chemistry of your nervous system (neurotransmitter balance). Yeast is another common problem. Yeast can damage the small intestine and cause it to become leaky and inflamed. Finally we have parasites; left untreated, parasitic infection can destroy your efforts to heal your digestive tract. You can’t assume that taking a probiotic will balance your gut if you have harmful microbes living in your bowels. Many digestion problems such as gas, bloating and IBS (irritable bowel syndrome) can be traced back to gut microbe problems.


If you want to optimize your digestive health, it is important to know if you are suffering from inflammation. Inflammation can have many causes including bacteria and yeast imbalance, parasitic infection, food sensitivity or allergy and leaky gut. Lack vitamins, minerals and antioxidants can also lead to increased inflammation of the digestive tract and your entire body.

Stool tests can measure the various types and amounts of SCFAs (short-chain fatty acids). Recently, there has been a lot of talk about prebiotics (not to be confused with probiotics).  


Prebiotics: a non-digestible fiber that goes through the small intestine and reaches the large intestine. This fiber is fermented in the bowel and feeds beneficial bacteria and acts as a fuel source for the cells that line the large intestine (colon).

Probiotic: are live beneficial bacteria and yeast. We get probiotic from our food as well as from dietary supplements.

SCFAs or Short Chain Fatty Acids are the end products of fermentation of dietary fibers by the intestinal microorganisms. SCFAs are important for your colon health and immune system.


A functional stool test can help your doctor gain a better understanding of what is working and what is not working with your digestive tract. In our Naperville office we frequently use this type of stool test as part of a comprehensive, gut-restoration program.

Many health problems originate from poor health of the digestive tract and the right kind of stool test can provide vital information required to restore optimal digestion function.

I wish you success on your quest for health!

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This approach to healthcare is not intended to diagnose, treat, cure, mitigate, or prevent any disease. Why? The FDA enforces its position that these words can only be used with drugs. This approach does not use drugs.