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The 4 Most Commonly Ordered Functional Medicine Lab Tests

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The 4 Most Commonly Ordered Functional Medicine Lab Tests

Lab tests help clarify a patient's condition and reveal the steps needed to establish health. Functional labs, specifically, can help practitioners dig deeper and get a more thorough look at what is happening in the whole person. Not only do practitioners benefit from the data, but patients also gain insight into why they feel the way they do.

Functional medicine practitioners use functional labs alongside patient history and symptom review to evaluate body system imbalances holistically. The labs are a vital piece to a thorough functional health assessment.


What is Functional Medicine?

Functional medicine is more than just alternative medicine. It is a form of medicine that helps to resolve complex and chronic health issues. It is surging into the mainstream as patients and practitioners seek a better way to approach healthcare.

Functional Medicine is an individualized, root-cause medicine approach to healthcare. Functional medicine practitioners differ in that they consider factors like diet, genetics, hormonal changes, and other lifestyle components as potential causes and treatments for patients' diseases. Functional medicine appointments are much more in-depth than typical allopathic appointments. They include a detailed intake and a series of specialty labs to overview how well your body is performing comprehensively.

Why Practitioners Order Functional Medicine Lab Tests

Functional medicine practitioners recognize that test results within standard lab ranges may be insufficient information to understand a patient's condition. Many patients are told that their labs are "within normal range," yet they still experience symptoms.

Instead, functional medicine practitioners order more in-depth functional labs to get a better look. However, even on routine blood work, functional medicine practitioners evaluate results in a narrower range known as the optimal range to catch certain markers early on. This way of practicing allows practitioners to reverse or stop disease progression altogether.

Most routine bloodwork is a general look at what is going on. Though helpful, it lacks specificity in pinpointing exactly where your system is off. Functional labs are fantastic for identifying specific areas that may be a problem. Every patient has their own unique biochemistry, genetics, and health condition. Specialty labs serve to narrow down where therapy must be applied to bring back balance to your systems.

From seeing hundreds of practitioners order functional labs from 30+ labs through our Lab Portal, these are the lab tests we have most often seen ordered for patients.

Rupa Health's Top 4 Comprehensive Stool Test

These tests are popular with providers because the gut is essential in functional medicine methodology.

Comprehensive stool tests look at many biomarkers, including those for:

  • Digestion and absorption levels
  • Inflammation levels
  • Presence of parasites and worms
  • The gut microbiome breakdown
  • Bacteria including H. Pylori, Campylobacter, Clostridium difficile

What's interesting is that providers often order one of these tests even if patients aren't directly complaining of GI symptoms. In one provider's words, "I order this for every single one of my patients because it helps me understand what's going on in the body from a root cause perspective - looking at the gut can give a unique insight into overall health." Stool testing has become popular because of the substantial research on the microbiome and its role in overall health.

GI Map

Diagnostic Solutions uses a unique technology in their GI MAP that can screen for low-level microbes. It tests over 50 pathogens, including bacteria, parasites, fungi, yeasts, H-pylori, and viruses. Therefore, this test is excellent if a gut infection is suspected.

Test highlights:

  • Gut microbial conditions- it tests the genetic potential for gut toxicity based on identifying specific strains of microorganisms
  • Digestion/Absorption- it tests imbalances in elastase and steatocrit, indicating pancreatic digestive function and fat digestion, respectively
  • Inflammation- it tests calprotectin and secretory IgA, which will indicate involvement of the inflammatory response from the gut mucosa

GI Effects Comprehensive Profile

As the name of this test implies, the GI Effects test by Genova Diagnostics offers a comprehensive look at gut function. Plus, it offers several add-on options to help personalize each order to the patient's needs. The GI Effects can provide a good start to gut analysis when there are several different gut issues.

Test highlights:

  • Gut microbial conditions- through a dual analysis method (PCR and stool culture), it screens for 24 types of bacteria and 30 different parasites; the presence of beneficial bacteria is also tested by assessing short-chain fatty acids
  • Digestion/Absorption- it detects the amount of undigested fat and broken-down proteins
  • Inflammation- it measures three possible sources of inflammation in calprotectin, secretory IgA, and eosinophil protein X

Comprehensive Stool Analysis + Parasitology - 3 Day

The Comprehensive Stool Analysis plus Parasitology test by Doctor's Data offers the same in-depth discovery of gut function as the other most popular tests. However, it differs because the three-day collection method provides more opportunities to find evidence of hard-to-detect parasites. Even more, it tests for antimicrobial susceptibility to prescription and natural agents.

Test highlights:

  • Gut microbial conditions- it comprehensively analyzes bacteria, yeasts, and parasites
  • Digestion/Absorption- it tests the standard carbohydrate, protein, and fat breakdown
  • Inflammation- it measures lactoferrin, calprotectin, and lysozyme

GI 360

The GI 360 stool test from Doctor's Data offers a solid look at gut function along with a highly detailed view of the microbiome. There is little this test doesn't cover regarding the GI tract.

Test highlights:

  • Gut microbial conditions- it tests by screening both pathogenic and commensal microbes; it screens for over 80 microorganisms, including mycoplasma, which isn't often considered in other tests
  • Digestion/Absorption- it tests by screening for incomplete digestion of proteins, carbohydrates, and fats
  • Inflammation- it tests through the standard markers for inflammation (calprotectin and secretory IgA) with the addition of lysozyme and lactoferrin

Rupa Health's Top 5 Female Health Panels

Balanced estrogen, progesterone, testosterone, and adrenal hormones are needed for fully functional health. The optimal levels will differ for each patient depending on their stage of life. Conventional labs look only at blood. However, a complete hormonal picture can be ascertained by testing saliva and urine.  

DUTCH Complete

Like the stool test, the DUTCH Complete (Dried Urine) by Precision Analytical is popular because rather than just checking for a "green flag" or "red flag" for a specific biomarker, it is a comprehensive view into how a person's adrenal and sex hormones are working together. These functional medicine lab tests help providers understand what's going on in the body and paint a larger picture rather than assigning "good" or "bad" levels in isolation.

Test highlights:

  • Includes analysis of oxidative stress, melatonin, and eight organic acids related to hormonal function
  • 4 points of specific collection times to assess hormonal rhythms
  • Unique testing methods to account for monitoring the use of oral or vaginal hormones


The DUTCH Plus (Dried Urine and Saliva)s by Precision Analytical looks at the production of sex hormones and their metabolites, as well as their patterns and distributions, giving providers a visual result of the hormone pathways in a person's body. Precision Analytical offers a whole suite of hormone tests; however, the DUTCH Plus is the most comprehensive. We see providers shifting from other hormonal tests to this one at an increasing rate. The DUTCH Plus's stronghold comes from the addition of Cortisol Awakening Response (CAR) measurements, which brings in biomarkers from another critical piece of the hypothalamic-pituitary-adrenal axis (HPA axis).

Test highlights:

  • Combined analysis of the urine and saliva
  • Includes analysis of oxidative stress, melatonin, and eight organic acids related to hormonal function
  • Tests Cortisol Awakening Response and adrenal hormones to give a better look at the HPA axis

Hormone’s Panel

The Hormones Panel  test from Vibrant America tests 13 analytes that give insight into sex hormones and their associated biomarkers necessary for ideal women's health.

Test highlights:

  • Includes metabolites related to sex hormone function
  • Analyzes blood levels to see the hormones in circulation

Saliva Profile III

ZRT Laboratory's Saliva Profile III - female/male offers an excellent baseline look at sex and adrenal hormones combined. Therefore, this is the perfect test to initiate hormonal testing.

Test highlights:

  • Gives a complete profile of 24-hour cortisol patterns through 4 samples collected during the day
  • A good test for monitoring hormone-supporting supplements and topical creams but not adequate for monitoring sublingual drops/troches

DUTCH Sex Hormones

The DUTCH Sex Hormone Metabolites (Dried Urine) test is Precision Analytical's offering on a solid baseline measurement for estrogen, progesterone, and androgen hormones and their metabolites. DUTCH Sex Hormone Metabolites assesses dried urine, making the sample stable for shipping.

Test highlights:

  • The testing method represents an entire 24-hour period of hormonal production
  • An accurate way to monitor the use of vaginal and oral hormone therapy


Rupa Health's Top 5 Nutrition Panels

Functional medicine is not simply an attempt to heal through supplements. A foundational piece is using food as medicine and ensuring the body properly processes all nutrients. Nutritional labs help identify problems in the metabolic chain.

Organic Acids Test

Organic Acids (OAT) by Great Plains Laboratory, called an OAT test, is a metabolic snapshot of a patient's overall health. Typically, it is recommended as a baseline test after the initial appointment, especially if the patient is dealing with mood disorders, fatigue, digestive complaints, or weight issues.  

Test highlights:

  • Able to evaluate intestinal yeast and bacteria
  • Includes urinary markers to indicate vitamin and mineral levels, oxidative stress, and neurotransmitter levels

NutrEval Plasma

The NutrEval Plasma by Genova Diagnostics tests over 125 biomarkers and over 40 antioxidants, vitamins, minerals, amino acids, and fatty acids. This test provides an excellent nutrition evaluation for patients suffering from a chronic condition or who want to screen for specific nutrient deficiencies, such as Vitamin D, B12, or magnesium.

Test highlights:

  • A more accurate measure of amino acids if a patient has proteinuria, mood disorders, or an uncontrolled diet
  • A multifaceted look at metabolism by testing serum, whole blood, and urine


The Metabolomix+by Genova Diagnostics uses a combination of tests and methodologies to synthesize the results of vital nutritional biomarkers. The results of this test allow practitioners to target which nutrients are needed for each patient.

Test highlights:

  • A patient-friendly collection process that can be done entirely at home
  • Add-ons are available for genomic testing and toxicity screening

Micronutrients Profile

Micronutrients Panel This test from Vibrant America is the only test that can evaluate the extracellular and intracellular levels of vitamins and minerals. The micronutrients panel tests for 40 different vitamins and minerals, fatty acids, and amino acids. Plus, it tests levels of omega fatty acids and the omega-3 index.

Test highlights:

  • It evaluates serum, intracellular, and extracellular levels of nutrients
  • No fast is necessary before the blood draw

Micronutrient Test

SpectraCell's Micronutrient Test covers 31 of the most common nutrients analyzed in nutritional testing. Not only does the Micronutrient Test measure the levels of nutrients, but it also evaluates performance and functional deficiencies.

Test Highlights:

  • Recommended for those suffering from chronic disease or digestion issues
  • No fasting is required, but it is not recommended for patients under 18 years old

Rupa Health's Top 5 SIBO Test

Many patients come to functional medicine in frustration after many years of not getting answers from several practitioners. If a conventional doctor hasn't already ordered a SIBO test, it's one of the first functional tests ordered when patients are experiencing GI symptoms that might be SIBO-related.

Small Intestinal Bacterial Overgrowth (SIBO) occurs when bacteria enter the small intestine, which is usually sterile, and begin to colonize. When non-bacterial organisms produce methane, the condition is called Intestinal Methanogen Overgrowth (IMO). Both can cause a variety of common gastrointestinal symptoms. By measuring the release of hydrogen and methane in the breath, SIBO/IMO can be detected.

SIBO 2-Hour test

The SIBO 2-Hour from Genova Diagnostics measures the fermented gases methane, hydrogen, and carbon dioxide. The levels are measured from six samples over 2 hours.

Test highlights:

  • It measures two of the primary gases fermented by the gut microbiome: hydrogen and methane
  • It uses lactulose as the substrate

SIBO 3-Hour Test

The SIBO 3-Hour test is  the same test as the SIBO 2-hour from Genova Diagnostics but with a more extended sample period. This 3-Hour test is preferred for those with slower gastrointestinal transit time or constipation.

Test highlights:

  • It provides a more extended test period for assessing SIBO in slower transit times and those with constipation

Trio-smart SIBO test

The Trio-smart SIBO Breath Test by Gemelli Biotech gets its name because it measures all three primary gasses fermented by the gut microbiome (hydrogen, methane, and hydrogen sulfide). This allows for a different perspective on testing SIBO, especially for patients with severe GI issues who test in the normal range on hydrogen and methane alone.

Test highlights:

  • A more comprehensive look at all three intestinal microbiome gases
  • It uses glucose as a test substrate instead of lactulose

SIBO/IMO Glucose Breath Test

The SIBO/IMO Glucose Breath Test is Commonwealth Diagnostics' offering to evaluate the fermented gases in the gut. It tests for the presence of carbon dioxide, methane, and hydrogen.

Test highlights:

  • Ten samples are collected over a period of 135 minutes
  • Glucose is used as the substrate for those with allergies or intolerance to lactulose

SIBO/IMO Lactulose Breath Test

The SIBO/IMO Lactulose Breath Test test from Commonwealth Diagnostics is the same as their SIBO/IMO Glucose Breath test. However, this test uses lactulose as the substrate instead of glucose.

Test highlights:

  • Ten samples are collected over a period of 135 minutes
  • It uses the industry standard substrate, lactulose

Rupa Health's Top 5 Food Sensitivity Panel

Nearly every lab company offers some version of IgG food sensitivity testing. The methodology for processing these tests differs by lab and the sample type can vary from an at-home blood spot to a full in-lab blood draw.  

Food sensitivity is not the same condition as having a food allergy. Food sensitivities are not life-threatening, like food allergies. However, testing them is a valuable tool in determining imbalances in gut function, and the inflammation they cause impacts overall health.

IgG Food MAP with Candida + Yeast

The IgG Food MAP from Great Plains Laboratory measures the antibodies of 190 common foods. This test goes beyond only testing IgG4 molecules and tests the total IgG antibodies.

Test highlights:

  • It measures 190 of the most common foods, including those from Western, Asian, and Mediterranean diets
  • It tests total IgG and screens for antibodies to Candida for current or past infections
  • It is available as a blood spot test for accessible at-home collection

96 IgG Food Sensitivity Panel

Alletess Medical Laboratory offers the 96 IgG Food Sensitivity Panel as an excellent way to evaluate patients when they present with common food sensitivity symptoms.

Test highlights:

  • It measures 96 of the most common foods
  • It is available as a blood spot or serum test

96 General Food Panel:  IgG

The 96 General Food test from US BioTek analyzes the IgG and IgA response to 96 common foods. The antibodies to Candida are also included, as chronic yeast infections may lead to food sensitivities.

Test highlights:

  • It measures IgA, IgG4, and total IgG antibodies to 96 foods
  • It is available as a blood spot or serum test

Array 4

Sometimes patients, especially those with Non-Celiac Gluten-Sensitive (NCGS) or Celiac Disease (CD), don't respond to eliminating gluten from their diets. The Array 4 serum test from Cyrex Laboratories helps identify additional foods that contain proteins that cross-react with gluten.

Test highlights:

  • It's an ideal test for Non-Celiac Sensitivity or Celiac patients
  • It's beneficial for patients with gut dysbiosis but who appear resistant to standard therapy or who have limited improvement on a gluten-free diet

P88 Dietary Antigen Test

The P88 Dietary Antigen by Precision Point is a unique test that combines IgE, IgG, IgG4, and complement (C3d) responses to 88 common foods. By testing these 4, the P88 DAT is valuable in finding food sensitivities and allergies.

Test highlights:

  • It's a comprehensive analysis of the immune response to 88 foods
  • It's available as a finger stick or serum test



By focusing on a narrower lab range, known as the optimal lab range, practitioners can detect dysfunction before overt diseases present. However, functional labs are a precision tool in the hands of a functional medicine practitioner. They help practitioners take a deeper, more holistic look into the body. This preventative approach helps patients who are seeking answers about their health. And for those already in the disease process, more precise answers and hope are available through functional medicine lab analysis.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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