If you’ve been dealing with bloating, IBS, reflux, or gut issues that won’t go away, you might be wondering:

“Should I get a colonoscopy? Or an endoscopy? Or something else?”

Maybe your doctor has already run tests, and everything came back “normal.” But deep down, you know something is off—your digestion feels unpredictable, food isn’t sitting right, and you’re constantly troubleshooting what’s causing your symptoms.

This is where functional stool testing, like the GI-MAP (what I use with clients in practice), can help uncover what’s going on beneath the surface. I would say it’s one of the most powerful tools I have to get people feeling remarkably better.

So, how do you know if you need a GI-MAP or a colonoscopy/endoscopy?

 

What Is a GI-MAP Stool Test?

The GI-MAP (Gastrointestinal Microbial Assay Plus) is a functional medicine stool test that uses DNA-based testing to analyze your gut microbiome, digestion, and inflammation levels—things that don’t show up on a colonoscopy.

What Does the GI-MAP Test For?

• Gut Dysbiosis & Microbiome Imbalances – Identifies good vs. bad bacteria and whether your gut is balanced.
• Parasites, Yeast & Fungal Overgrowth – Looks for infections like Candida, LPS (endotoxin)-producing bacteria, or dientamoeba fragilis parasite that may be causing bloating, fatigue, or cravings.
• H. pylori & Stomach Acid Production – Detects H. pylori, a bacteria linked to reflux, ulcers, and low stomach acid, which can lead to bloating, poor digestion, and increases the risk of other overgrowth like SIBO.
• Leaky Gut & Gut Inflammation – Measures markers like zonulin (a marker for leaky gut), secretory IgA (gut’s immune system) calprotectin (inflammation marker) to see if your gut lining is compromised.
• Digestive Enzyme Function – Checks if your pancreas is producing enough enzymes to properly digest fats and proteins.

Who Should Consider a GI-MAP Stool Test?

• Ongoing bloating, constipation, or diarrhea
• Food sensitivities that seem to be getting worse
• Acid reflux, nausea, or floating stool
• Skin issues like eczema, acne, or rosacea that could be linked to gut health
• Chronic fatigue, brain fog, or joint pain that hasn’t improved with diet changes

The GI-MAP is a non-invasive test that can be done at home without the need for a doctor’s office visit.

 

What Is a Colonoscopy or Endoscopy?

A colonoscopy or endoscopy is a medical procedure that allows a gastroenterologist to visually examine the inside of your digestive tract to check for structural issues like ulcers, inflammation, or polyps.

What Do These Procedures Check For?

• Colonoscopy – Screens for colon cancer, polyps, and inflammation in the large intestine.
• Endoscopy – Examines the esophagus, stomach, and upper small intestine for ulcers, GERD damage, or abnormal growths.

Who Should Consider a Colonoscopy or Endoscopy?

• Severe abdominal pain or unexplained weight loss
• Blood in stool or rectal bleeding
• Family history of colon cancer
• Chronic acid reflux that isn’t improving with diet or lifestyle changes
• Adults over the age of 45 (typically when regular screenings are recommended)

These are necessary medical procedures when symptoms indicate a serious condition.

 

Why a GI-MAP Stool Test Can Fill the Gaps in Gut Health Testing

A colonoscopy or endoscopy is important for ruling out serious issues like ulcers, tumors, or structural problems, but it won’t tell you:

• What bacteria or pathogens are in your gut
• If you have leaky gut or inflammation
• If your stomach acid is too low
• If your microbiome is imbalanced
• How well your body is breaking down food

A GI-MAP provides this information—so if you’ve been told, “everything looks fine,” but you don’t feel fine, this test might give you the answers you’ve been missing.

 

So, Which Test Should You Get?

• If you’re experiencing severe symptoms like unexplained bleeding, pain, or weight loss, a colonoscopy or endoscopy is necessary to rule out anything serious.
• If you have ongoing gut issues that aren’t resolving, a GI-MAP stool test can uncover the root cause and help you start healing.
• If your doctor has told you, “nothing is wrong,” but you’re still struggling, the GI-MAP is worth considering.

 

How to Get a GI-MAP Stool Test

This is a functional medicine test, which means it’s not something you’ll get at a routine doctor’s visit. It’s typically ordered through a functional medicine nutritionist (hello!) or a practitioner specializing in gut health.

If you’re looking for answers about your gut health, microbiome, and digestion, I can help you decide if the GI-MAP stool test is the right next step via a free intro call here.