Introduction In recent years, gut microbiome testing has become more accessible through at-home kits that analyze stool samples to profile bacteria, viruses, and fungi in the digestive tract. These tests can offer insights into dysbiosis, inflammatory signals, and metabolite production using techniques such as 16S rRNA or metagenomic sequencing. Costs vary by depth of analysis and services, typically ranging from about $100 to $400 or more depending on lab methods and reporting features. FSA and HSA Basics for Diagnostic Tests Flexible Spending Accounts (FSAs) and Health Savings Accounts (HSAs) both allow pre-tax funds to be used for qualified medical expenses. Under IRS guidance, an expense is generally eligible when it is primarily for the diagnosis, mitigation, treatment, or prevention of disease. That means microbiome testing may be reimbursable when it is used to evaluate or manage a specific medical condition rather than for general wellness. When a test is recommended by a clinician to investigate symptoms such as chronic bloating, persistent diarrhea, suspected small intestinal bacterial overgrowth (SIBO), or unexplained systemic symptoms, documentation (a prescription or letter of medical necessity) strengthens the claim for FSA/HSA coverage. Without such documentation, administrators often classify tests performed for general curiosity as non-covered. Practical Steps to Improve Reimbursement Odds - Consult your healthcare provider first and, if appropriate, request a prescription or letter of medical necessity that explains how the test relates to diagnosis or treatment. - Keep itemized receipts that show the provider name, date, service description, and cost. - Check with your FSA/HSA administrator or HR — administrators vary in interpretation and documentation requirements. - Use scientifically validated test providers that supply clear invoices and results summaries; these documents make it easier to justify medical necessity if requested. Types of Tests and What You’re Paying For Basic 16S rRNA tests identify bacterial genera and are generally less expensive. Shotgun metagenomic sequencing provides species-level resolution and captures viruses and fungi as well, and is priced higher due to greater lab complexity. Many reports also include interpretive content or clinician access, which can add to cost. Consider whether the analysis depth aligns with your clinical question when deciding whether to pursue reimbursement. Resources and Further Reading For more detail on how specific microbiome services present results and documentation, you can review the test provider overview at [Innerbuddies microbiome test](https://www.innerbuddies.com/blogs/gut-health/fsa-hsa-gut-microbiome-test). Additional, relevant reading includes an overview of beneficial gut bacteria at Beneficial Bacteria — Your Gut’s Natural Defenders and a practical nutrition guide at A Gut Health Diet That Actually Works. A supplementary primer is available on Telegraph: Personalized Nutrition with InnerBuddies (Telegraph). If you need specific documentation templates or wording for a letter of medical necessity, many HSA/FSA administrators or clinical offices can provide guidance. Using pre-tax funds for diagnostic testing is feasible when the test supports medical care and is properly documented.