I had a period last year where I was bloated after nearly every meal. Not the mild "I ate too much" bloating. The uncomfortable, distended, something-is-wrong kind. It lasted about six weeks before I mentioned it to my GP.
She asked two questions that reframed my thinking. First: "Does anyone in your family have coeliac disease?" (No, not that I know of.) Second: "Have you ever been tested?" (No.)
She ordered a coeliac antibody screen alongside a few other markers. The result came back negative. I don't have coeliac disease. But the experience was useful for two reasons. First, it ruled out a condition that affects roughly 1 in 70 Australians, 80% of whom are undiagnosed. Second, it made me realise how little I actually understood about what blood tests can and can't reveal about gut health.
"Gut health" is one of the most searched health topics in Australia. It's also one of the most commercially exploited. The wellness industry has built an entire ecosystem around the microbiome: probiotics, prebiotics, gut cleanse protocols, elimination diets, functional testing panels. Some of this is evidence-based. A lot of it isn't. And the gap between the marketing and the medicine is wide enough to drive a supplement company through.
This article tries to bridge that gap. It covers what blood tests can genuinely detect about gut function, including coeliac disease, inflammation, and the nutritional consequences of gut dysfunction. It also covers where stool-based testing fits in. It's not a microbiome deep-dive. It's a practical guide to which blood markers matter and why.
A note before we get into it
General information only. I'm not a gastroenterologist. Gut conditions can be complex and require specialist investigation including imaging, endoscopy, and biopsy. Blood tests are a screening and monitoring tool, not a complete diagnostic workup.
If you have persistent digestive symptoms (bloating, pain, diarrhoea, constipation, blood in stool), see your GP. Some gut conditions require urgent investigation.
"Gut health" as wellness trend vs clinical reality
I want to draw a line early in this article between two very different conversations.
Conversation 1 (wellness): "Your gut is your second brain. Heal your gut and you heal everything. Take this probiotic. Do this cleanse. Test your microbiome diversity score." This conversation is everywhere. Instagram, podcasts, supplement brands. Some of the underlying science is real (the gut-brain axis exists, the microbiome does influence health). But the leap from "the microbiome is important" to "buy this product to fix yours" is often several evidence gaps wide.
Conversation 2 (clinical): "Does this patient have coeliac disease? Is there inflammation in the GI tract? Are nutrient absorption issues causing measurable deficiencies? Is there a structural or functional problem that needs investigation?" This conversation happens in your GP's office and produces actionable answers.
Blood tests operate firmly in Conversation 2. They can't map your microbiome. They can't tell you whether your gut "flora" is balanced (whatever that means). But they can detect autoimmune gut conditions, systemic inflammation, and the nutritional fallout from poor gut function. Clinically, those are the things that actually matter.
What blood tests can actually tell you about your gut
Blood tests offer three windows into gut health:
1. Autoimmune detection. Specifically coeliac disease, the most common autoimmune gut condition and one of the most underdiagnosed conditions in Australia.
2. Inflammation assessment. Markers like CRP and ESR indicate systemic inflammation, which can originate from gut pathology including inflammatory bowel disease (Crohn's, ulcerative colitis) and other conditions.
3. Nutritional consequences. If your gut isn't absorbing nutrients properly, the deficiencies show up in blood work. Iron, B12, folate, vitamin D, and zinc are all absorbed through the gut. Persistently low levels despite adequate intake can signal an absorption problem.
These three windows don't diagnose specific gut conditions (with the exception of coeliac serology). But they create a clinical picture that guides further investigation.
Coeliac disease: Australia's most underdiagnosed autoimmune condition
This section could be its own article. Coeliac disease is that common and that misunderstood.
What it is. An autoimmune condition where the immune system reacts to gluten (a protein in wheat, barley, rye, and oats), causing inflammation and damage to the lining of the small intestine. Over time, this damage impairs nutrient absorption and can lead to a range of complications.
How common it is. Approximately 1 in 70 Australians have coeliac disease, with WEHI research estimating 1 in 60 women and 1 in 80 men. Despite this, around 80% remain undiagnosed. That means hundreds of thousands of Australians are walking around with an autoimmune condition damaging their gut lining, and they have no idea.
Why it's so commonly missed. The symptoms are maddeningly nonspecific. Bloating, fatigue, diarrhoea or constipation, abdominal pain, iron deficiency, brain fog, mouth ulcers, joint pain, skin rashes. Many people with coeliac disease are asymptomatic or have such mild symptoms that they never think to investigate. Others are misdiagnosed with irritable bowel syndrome, food sensitivities, or "stress."
The genetic piece. About 50% of Australians carry the HLA-DQ2 and/or HLA-DQ8 genes, which are necessary (but not sufficient) for coeliac disease to develop. Having the genes doesn't mean you'll get it, but without them, coeliac disease is essentially ruled out.
First-degree relatives have a 10% chance of also having coeliac disease. If a parent, sibling, or child has been diagnosed, screening is strongly recommended.
The blood test. Coeliac serology measures antibodies produced by the immune system in response to gluten. The primary test is tissue transglutaminase IgA (tTG-IgA). Total IgA is usually tested alongside it because about 2-3% of people with coeliac disease have IgA deficiency, which can produce false-negative results on IgA-based tests.
You must be eating gluten when you test. If you've already eliminated gluten from your diet, the antibodies may not be detectable even if you have coeliac disease. This is one of the most common testing errors. People go gluten-free, feel better, and then test for coeliac disease, producing a false negative.
Confirmation. A positive blood test is typically followed by a duodenal biopsy (via gastroscopy) to confirm the diagnosis by examining the intestinal lining for damage.
Inflammation markers and gut health
CRP (C-Reactive Protein)
What it tells you
An elevated CRP indicates systemic inflammation. It's not specific to the gut. CRP rises with infection, autoimmune disease, metabolic syndrome, and many other conditions. But in the context of digestive symptoms, elevated CRP adds weight to the case for further gut investigation.
High-sensitivity CRP (hs-CRP) detects lower-grade inflammation and may be relevant for chronic, smouldering gut issues. However, CRP alone doesn't tell you where the inflammation is coming from.
Test it with Bloody Good:
Full Blood Count (FBC)
The gut health angle
An FBC can reveal signs of inflammation (elevated white blood cells, elevated platelets) and anaemia (low haemoglobin, which may indicate chronic gut blood loss or malabsorption).
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ESR (Erythrocyte Sedimentation Rate) is another nonspecific inflammatory marker, sometimes used alongside CRP to build the inflammatory picture.
What inflammation markers can't do. They can't diagnose inflammatory bowel disease (Crohn's, ulcerative colitis) on their own. That requires specialist investigation, typically colonoscopy, imaging, and clinical assessment. But elevated inflammatory markers in someone with persistent gut symptoms strengthen the case for referral.
Nutritional markers as gut health signals
This is the under-appreciated angle. If your gut isn't absorbing nutrients properly, the evidence shows up in your blood work. Sometimes before gut symptoms are obvious.
Iron and Ferritin
Why it matters for gut health
Low ferritin is one of the most common presentations of undiagnosed coeliac disease. Iron is absorbed in the duodenum, exactly where coeliac disease causes the most damage. Unexplained iron deficiency, particularly when it doesn't respond to oral supplementation, should prompt coeliac screening.
I covered this in detail in the iron article.
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Vitamin B12
Why it matters for gut health
B12 is absorbed in the terminal ileum. Low B12 can signal malabsorption from Crohn's disease (which often affects the ileum), gastric conditions, or pernicious anaemia.
More detail in the B12 article.
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Folate
Why it matters for gut health
Folate is absorbed in the upper small intestine. Low folate alongside iron deficiency raises suspicion of coeliac disease or other small bowel pathology.
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Vitamin D
Why it matters for gut health
Vitamin D is absorbed in the small intestine. Low vitamin D despite adequate sun exposure or supplementation may indicate a gut absorption problem.
More detail in the vitamin D article.
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Zinc
Why it matters for gut health
Zinc is absorbed throughout the small intestine. Low zinc alongside other nutritional deficiencies suggests broad malabsorption.
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The pattern matters more than individual markers. One low nutrient could be dietary. Multiple low nutrients (iron plus B12 plus folate plus vitamin D) in someone with gut symptoms is a strong signal that absorption is compromised and the gut needs investigation.
Blood tests vs stool tests: what each does
Bloody Good offers both blood-based and stool-based gut testing. They answer different questions.
| Blood tests tell you | Stool tests tell you |
|---|---|
| Whether coeliac antibodies are present | The composition of your gut microbiome (diversity, specific bacterial species) |
| Whether systemic inflammation exists (CRP) | Whether there's gut-specific inflammation (calprotectin) |
| Whether nutrient absorption is impaired (iron, B12, folate, vitamin D, zinc) | Whether certain pathogens or parasites are present |
| Signs of chronic blood loss or immune activation (FBC) | Markers of digestive function (elastase, short-chain fatty acids) |
Blood tests first if you suspect coeliac disease, have unexplained nutritional deficiencies, or have symptoms alongside other systemic issues (fatigue, joint pain, skin problems). Blood tests are the clinical starting point.
Stool tests if you want a deeper picture of your microbiome composition, have symptoms suggestive of inflammatory bowel disease (bloody diarrhoea, persistent abdominal pain), or are working with a practitioner on gut health optimisation. Stool-based calprotectin is particularly useful for distinguishing inflammatory bowel disease from irritable bowel syndrome.
Both if you want a thorough gut assessment. The blood markers screen for systemic issues. The stool markers assess the gut environment itself.
Who should be testing
Anyone with persistent digestive symptoms (bloating, pain, altered bowel habits, reflux) that haven't been adequately investigated.
Anyone with unexplained iron deficiency, especially if it doesn't respond to oral supplementation. Coeliac screening should be standard in this situation.
First-degree relatives of someone with coeliac disease. 10% risk. Screening is recommended even without symptoms.
People with other autoimmune conditions. Type 1 diabetes, autoimmune thyroid disease (Hashimoto's, Graves'), and other autoimmune conditions are associated with higher coeliac disease risk.
People with unexplained fatigue alongside nutritional deficiencies. The combination of fatigue plus low iron plus low vitamin D plus low B12, without an obvious dietary cause, should prompt gut investigation.
Anyone who's gone gluten-free without first testing for coeliac disease. This is common. If you eliminated gluten and felt better, you may have coeliac disease, but you can't test accurately while gluten-free. Discuss a gluten challenge with your GP if you want to investigate.
How to prepare
For coeliac serology: You must be consuming gluten. The recommendation is to consume gluten (equivalent to about 2-4 slices of bread daily) for at least 6 weeks before testing. If you've been gluten-free, discuss a gluten challenge with your GP before ordering the test.
For iron studies: Fast for 8-12 hours. Stop iron supplements 24-48 hours before.
For CRP and other inflammation markers: Avoid testing when acutely unwell. Infection and injury can transiently elevate CRP.
For the stool-based microbiome test: Follow the kit instructions carefully. Collection timing and storage matter for sample integrity.
Tests to consider through Bloody Good
| Test | What it covers | Category |
|---|---|---|
| Coeliac Antibodies | tTG-IgA screening (must be on a gluten-containing diet) | Gut-focused |
| High-Sensitivity CRP | Systemic inflammation marker | Gut-focused |
| Full Blood Count (FBC) | Anaemia and inflammatory markers | Gut-focused |
| Iron Studies (Including Ferritin) | Most common nutritional marker of gut pathology | Nutritional |
| Vitamin B12 | Ileal absorption assessment | Nutritional |
| Folate | Small intestinal absorption | Nutritional |
| Vitamin D (25-OH) | Fat-soluble vitamin absorption | Nutritional |
| Zinc | Broad absorption marker | Nutritional |
| Gut Health Microbiome Stool Test Kit | Microbiome analysis, pathogen screening, functional markers | Stool-based |
If you'd rather cover everything at once:
The Bloody Good Test covers 100 blood biomarkers including iron studies, B12, folate, vitamin D, FBC, CRP, liver function, and more. Combining this with the coeliac antibody test and the stool-based microbiome kit provides the most thorough gut health assessment available through the platform.
What to do after testing
If coeliac antibodies are positive: See your GP for referral to a gastroenterologist. Diagnosis is typically confirmed with a duodenal biopsy. Do not start a gluten-free diet before biopsy confirmation. Removing gluten can heal the intestinal damage and make biopsy results inconclusive.
If coeliac is negative but symptoms persist: Coeliac serology is highly sensitive but not perfect. If clinical suspicion remains high, your GP may recommend further investigation, including genetic testing (HLA-DQ2/DQ8 to rule out coeliac entirely) or endoscopy. IBS, food intolerances, SIBO (small intestinal bacterial overgrowth), and functional gut disorders are all in the differential.
If inflammation markers are elevated: In the context of gut symptoms, this warrants further investigation. That could include calprotectin testing (stool-based), imaging, or colonoscopy referral.
If nutritional markers show a malabsorption pattern: Multiple deficiencies (iron plus B12 plus folate plus vitamin D) despite adequate dietary intake strongly suggest a gut absorption problem. Coeliac screening is a must if not already done. Further investigation may include endoscopy and small bowel assessment.
If everything's normal: Good news. The common gut pathologies have been screened and your nutrient absorption appears intact. If symptoms persist, consider the stool-based microbiome assessment for functional gut insights, or discuss IBS management with your GP. Dietary strategies (low-FODMAP under dietitian guidance, for example) may be appropriate.
Explore more biomarkers
If you want to go deeper into any of the markers covered here, the Bloody Good biomarker directory has detailed pages on what each test measures and how to think about results in general terms.
Browse the Bloody Good Biomarker Directory
This article provides general health information only and is not intended as medical advice, diagnosis, or treatment. Blood test results should be interpreted by a qualified healthcare professional in the context of your individual health circumstances, including symptoms, medical history, and medications. If you are experiencing persistent or concerning symptoms, consult your GP or seek medical attention promptly.