Introduction

Gut microbiome testing is increasingly used to inform clinical decisions and personalized nutrition strategies. These tests analyze bacteria and other microorganisms in stool samples to identify imbalances that may be associated with conditions such as irritable bowel syndrome (IBS), persistent bloating, food sensitivities, and some inflammatory disorders. Because many kits cost between $100 and $350, patients commonly ask whether Health Savings Accounts (HSAs) or Flexible Spending Accounts (FSAs) can cover the expense.

When a Microbiome Test May Be Eligible

The Internal Revenue Service (IRS) allows HSAs and FSAs to reimburse qualified medical expenses used for the diagnosis, cure, mitigation, treatment, or prevention of disease. In practice, diagnostic lab tests recommended by a licensed healthcare provider are often eligible if there is medical necessity. A Letter of Medical Necessity (LMN) documenting the condition and why the test is required substantially strengthens a reimbursement claim.

Tests purchased strictly for general wellness or curiosity are less likely to qualify. Conversely, when a clinician orders microbiome testing to investigate specific gastrointestinal symptoms or to guide treatment decisions, that diagnostic intent aligns more closely with IRS definitions of qualified medical expenses.

Documentation and Reimbursement Process

To pursue reimbursement, patients typically need: (1) a dated LMN or physician order describing the medical condition and purpose of the test, (2) an itemized receipt showing the provider and services rendered, and (3) the final report if requested by the plan administrator. Many HSA/FSA administrators permit retrospective claims when supported by documentation, but rules and requirements vary by plan.

Providers and lab methodologies can influence acceptance. Tests that include laboratory accreditation, clear methodology (for example, 16S rRNA sequencing or metagenomic analysis), and clinician-oriented reports are more likely to be treated as diagnostic rather than purely wellness-oriented.

Plan Variability and Verification

Not all HSA or FSA administrators treat the same services identically. It is advisable to check the plan’s eligible expense list and speak with member services before purchasing. For examples of how gut-focused topics intersect with testing and seasonal factors, see the article on how plant-based diets affect gut health at plant-based diets can keep your gut happy and the discussion of seasonal variation in test results at how seasonal changes impact your gut microbiome test results.

For additional context on seasonality and microbiome measurement, a concise overview is available at How Do Seasonal Changes Impact Your Gut Microbiome Test Results.

Practical Recommendations

Before purchasing a kit, confirm whether your healthcare provider will provide the documentation needed for reimbursement and whether your HSA/FSA administrator recognizes the vendor and test type. If you need further product details to share with a clinician or administrator, consider using the microbiome testing kit specification page at microbiome testing kit to support your inquiry.

In summary, gut microbiome testing can be HSA- or FSA-eligible when ordered or documented by a healthcare professional for a specific medical purpose; verifying plan rules and obtaining appropriate documentation are key steps to secure reimbursement.

For guidance on whether a particular purchase qualifies under your plan, review official plan documents or consult your HSA/FSA administrator. More detailed guidance can be found in our article explaining the reimbursement criteria at Can I Use HSA or FSA to Pay for a Gut Microbiome Test?.