Functional Medicine Tests We Use At The Autoimmune Clinic To Support Clients With Complex Chronic Illness

One of the most common questions we get asked is: "What tests do we use and what tests should YOU do?"

In functional medicine, testing can be incredibly valuable, but only when it is used appropriately and interpreted in the context of a person's symptoms, medical history, environment and lifestyle. A test result in isolation rarely tells the whole story.

Over the years, there are certain investigations that we find ourselves returning to again and again when working with complex chronic illness, autoimmunity, fatigue, digestive issues, histamine intolerance, mast cell activation syndrome (MCAS), mould illness and unexplained symptoms.

So here are some of the most common tests we use at The Autoimmune Clinic.

1. Comprehensive Blood Work Before Functional Medicine Testing

This is always our starting point.

Before considering expensive private testing, we want to ensure that the foundations have been covered properly.

Many clients arrive having had only limited blood work performed, despite experiencing symptoms for years. It is not uncommon for important markers to have been overlooked.

We typically like to assess:

• Full Blood Count: Haemoglobin, haematocrit, RBC, MCV, MCH, WBC, neutrophils, lymphocytes, monocytes, eosinophils, basophils, platelets

• Inflammation: CRP, ESR

• Thyroid Function: TSH, Free T4, Free T3, TPO antibodies, thyroglobulin antibodies

• Iron Status: Ferritin, serum iron, transferrin, transferrin saturation, TIBC

• Nutrient Status: Vitamin D, B12, folate, magnesium, zinc, copper

• Blood Sugar & Metabolic Health: HbA1c, fasting glucose, fasting insulin, C-peptide

• Liver Function: ALT, AST, ALP, GGT, bilirubin, albumin, total protein

• Kidney Function: Creatinine, eGFR, urea

• Electrolytes: Sodium, potassium, chloride, bicarbonate

• Lipids: Total cholesterol, LDL, HDL, triglycerides, non-HDL cholesterol

• Immune Markers: Total IgE, IgG, IgA, IgM

• Hormones (when appropriate): Testosterone, SHBG, oestradiol, progesterone, prolactin, DHEA-S, LH, FSH, Cortisol

Where possible, we utilise NHS testing through the GP and supplement this with private testing when required.

2. Autoimmune Screening

Autoimmune disease can develop long before a formal diagnosis is made.

Many individuals experience symptoms for years before sufficient tissue damage has occurred to meet conventional diagnostic criteria.

Depending on the individual's presentation, we may investigate:

• General Autoimmunity: ANA, ENA panel, dsDNA, complement C3 & C4

• Rheumatoid Arthritis: Rheumatoid Factor (RF), Anti-CCP antibodies

• Thyroid Autoimmunity: TPO antibodies, thyroglobulin antibodies, TSH receptor antibodies (TRAb) where appropriate

• Coeliac Disease: Tissue transglutaminase (tTG), endomysial antibodies (EMA), total IgA, coeliac genetics where indicated

• Inflammatory Bowel Disease: Faecal calprotectin, ASCA, ANCA where appropriate

• Liver Autoimmunity: Anti-mitochondrial antibodies (AMA), smooth muscle antibodies (SMA), LKM antibodies

• Connective Tissue Disease: SSA/Ro, SSB/La, RNP, Sm, Scl-70, Jo-1 and other ENA markers

• Type 1 Diabetes Risk: GAD65, IA-2 and ZnT8 antibodies where clinically relevant

Early identification can provide important clues and help direct further investigations and interventions.

3. VCS Testing and HLA Genetics

When Chronic Inflammatory Response Syndrome (CIRS) is suspected, we often start with two relatively accessible tests:

• Visual Contrast Sensitivity (VCS) Testing: The VCS test is a low-cost screening tool that assesses visual processing. Certain patterns may be associated with biotoxin-related illness.

• HLA Genetic Testing: We often combine VCS testing with HLA DRB1, DRB3, DRB4, DRB5 and DQB1 genetic testing.

These genes can help identify whether somebody may have increased susceptibility to difficulties clearing biotoxins from exposures such as mould, water-damaged buildings or certain infections.

Interestingly, we rarely see a negative result in clients we specifically choose to test, which reflects the population we tend to work with.

4. SIBO Breath Testing

Small Intestinal Bacterial Overgrowth (SIBO) is one of the most common findings we encounter.

For many of our clients, we often prioritise SIBO testing before stool testing because of the significant overlap between:

• SIBO

• Histamine intolerance

• Mast cell activation

• Autoimmune disease

• Chronic fatigue

• Skin conditions

Symptoms may include bloating, reflux, constipation, diarrhoea, abdominal pain, food intolerances and systemic inflammatory symptoms.

Identifying SIBO can often be a major turning point in understanding a person's health picture.

5. Stool Testing

Stool testing can provide valuable information, but it is important to recognise its limitations.

A stool test may offer insights into:

• Digestive capacity

• Inflammation

• Gut microbiome composition

• Potential bacterial, fungal or parasitic infections

• Immune activity within the digestive tract

However, no stool test is perfect.

One of the biggest mistakes we see is treating laboratory findings without considering whether they are actually relevant to the individual's symptoms.

We have seen many people placed on aggressive parasite or candida protocols that were ultimately unnecessary and failed to address the true drivers of their symptoms.

6. Infection Testing

For some individuals, chronic infections may be contributing to an already overloaded system.

Depending on the clinical picture, we may investigate:

• Tick-borne infections

• Lyme disease and associated co-infections

• Chronic viral infections

• Reactivation of latent viruses

• Spike protein levels where clinically appropriate

We often use the "bucket analogy" when explaining chronic illness.

Many factors can contribute to symptoms simultaneously. Chronic infections may represent one of several contributors filling the bucket until symptoms begin to appear.

7. In-Depth Immune and Allergy Testing

Standard blood tests provide useful information, but they do not always tell us how the immune system is functioning in more complex cases.

Advanced immune testing can help us assess whether the immune system appears:

• Suppressed

• Overactive

• Chronically activated

• Dysregulated

• Exhausted

We may decide to investigate:

• Total IgE

• Environmental allergies

• Dust mite sensitivity

• Mould allergies

• Animal allergies

• Pollen allergies

• Immunoglobulins (IgG, IgA, IgM)

• Lymphocyte subsets

• Immune status panels

These tests can sometimes reveal important drivers that have been overlooked for years.

8. Genetic Risk Testing

We commonly investigate genetic risk factors relating to:

• Coeliac Disease: Many people come to us clinic already following a gluten-free diet without having undergone proper coeliac screening. Genetic testing can help assess whether coeliac disease remains a possibility when standard testing is no longer reliable due to long-term gluten avoidance.

• Haemochromatosis: Raised ferritin is often automatically attributed to inflammation.

While this may be true, it is important not to overlook the possibility of hereditary iron overload disorders such as haemochromatosis.

Genetic testing can help clarify the picture.

9. CIRS Blood Biomarkers

If these tests were not so expensive in the UK, they would feature much higher on this list.

When routine blood tests appear normal, looking beyond standard markers can often provide valuable clues.

Conventional testing largely focuses on broad inflammation markers and the adaptive immune system. However, this only tells part of the story.

By assessing aspects of the innate immune system, we may identify patterns of chronic immune activation that would otherwise be missed.

Common markers include:

• TGF-β1

• C4a

• C3a

• MMP-9

• VEGF

• MSH

• ACTH and cortisol

• VIP

While these tests are not appropriate for everyone, they can be extremely informative in some cases.

10. DUTCH Testing

Hormones absolutely matter, but they are rarely where we start.

Hormones are highly influenced by the environment they are operating in. Factors such as inflammation, infections, poor sleep, blood sugar dysregulation, mould exposure, nutrient deficiencies and chronic stress can all affect hormone production and metabolism.

The DUTCH test provides a detailed assessment of:

• Oestrogen metabolism

• Progesterone

• Testosterone

• DHEA

• Cortisol patterns

For individuals who have already established strong foundations, or whose primary concerns relate to hormones, it can be an extremely useful investigation.

Now Remember: Functional Medicine Testing Is Only Part of the Story

The best test in the world is only useful when interpreted in the context of:

• Symptoms

• Medical history

• Environment

• Lifestyle

• Clinical presentation

Testing should support clinical decision-making, not replace it.

At The Autoimmune Clinic, our goal is not to collect as many test results as possible. Our goal is to understand what is driving your symptoms and identify the interventions most likely to help you move forward.

If you would like to explore whether testing could help make sense of your health concerns, feel free to get in touch and book a discovery call with one of our practitioners.

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At The Autoimmune Clinic, we specialise in helping people with autoimmune disease, chronic fatigue, digestive disorders, histamine intolerance, MCAS, mould-related illness, Long COVID, hormonal imbalances and other complex chronic health conditions.

Using a functional medicine approach, we look beyond individual diagnoses to understand the factors that may be driving symptoms, including immune dysfunction, gut health, infections, environmental exposures, nutritional deficiencies and nervous system dysregulation.

Our goal is to help clients make sense of their health challenges and create personalised, evidence-informed plans that address the root causes of illness.