top of page

The Truth About Stool Testing in Functional Medicine

In this post, I want to address a common concern I hear from prospective clients: the validity of stool testing. There are varying opinions in the functional medicine community about whether stool testing provides reliable data. Some practitioners, even those I've trained with, prefer not to use stool testing because they question its accuracy. I’d like to share my perspective, based on my experience and training as a Functional Diagnostic Nutrition Practitioner, to shed light on why I believe stool testing is a valuable tool, especially for those struggling with IBS and other gut issues.

Understanding the Skepticism

It’s true that not everyone in the functional medicine space endorses stool testing. Some practitioners argue that the data may not always be reliable. While no test is perfect, I’ve seen significant benefits from stool testing in my practice. It's not just about the numbers; it's about connecting the dots between a client's symptoms and the insights from their stool test results.

My Personal Experience

In my clinical practice, I’ve witnessed many positive outcomes from stool testing. These tests have helped uncover the underlying issues contributing to a client's symptoms, allowing us to develop more targeted and effective treatment plans. Recently, I consulted with a client who brought in a large number of supplements she was taking. Despite this, her IBS symptoms persisted. This is a common scenario where functional stool testing can provide crucial information that supplements alone cannot address.

The Value of Functional Stool Testing

For those considering a functional medicine approach to managing IBS, I believe functional stool testing is essential. Trying to guess what might be wrong without data is like throwing spaghetti at a wall and hoping it sticks. Stool tests provide concrete data that can guide effective treatment plans, ensuring that supplements and dietary changes are targeted and efficient.

Common Misconceptions About Supplements

Many clients come to me overwhelmed by the number of supplements they are taking. While supplements can be beneficial, relying solely on them without proper testing can become costly and ineffective. By running functional tests, we can validate the need for specific supplements and create a focused plan that aims to reduce long-term dependence on numerous products. My goal is to work clients down to a manageable number of supplements—ideally, three to five—that they might need to maintain long-term health.

Real-World Applications

Here are a couple of client cases where stool testing proved indispensable:

  1. Client with Hashimoto’s and Acid Reflux: Despite a strict elimination diet and efforts to manage gut health, her symptoms persisted. A GI map functional stool test revealed a protozoa parasite, Blastocystis hominis, which has a high correlation with thyroid issues like Hashimoto's. Addressing this parasite was key to reducing her thyroid antibodies and improving her overall health.

  2. Client with Hypothyroid Symptoms: This client also experienced unresolved gut issues and thyroid dysfunction. Functional stool testing helped identify hidden pathogens and digestive imbalances that standard tests missed. This data allowed us to create a targeted plan that significantly improved her symptoms.

The Strengths of Functional Stool Testing

Functional stool tests offer several key insights:

  • Microbiome Balance: Understanding the diversity and balance of beneficial and harmful bacteria in the gut.

  • Digestive Function: Assessing markers like bile quality and enzyme production to evaluate digestion.

  • Inflammatory Markers: Identifying levels of inflammation and potential autoimmune triggers.

  • Pathogen Detection: Detecting bacteria, parasites, and fungal overgrowth that might be causing chronic symptoms.

Acknowledging Limitations

While functional stool testing is valuable, it's important to recognize that no test is perfect. Tiny parasites, for instance, might not always be detected due to their location in the body or elimination patterns. Therefore, even if a test result doesn't show certain pathogens, we might still proceed with a treatment plan based on symptoms and other clinical data.


Functional stool testing can be a powerful tool for uncovering the root causes of gut health issues. It provides essential data that can guide effective treatment plans, helping to alleviate symptoms and improve overall health.

1 view0 comments


bottom of page