Current Regulation by Continent and Country
Rules differ from country to country; we map how the FDA, Health Canada, and Europe's member states handle FMT, from the strictest regimes to the most permissive.
North America
United States: The FDA classified FMT as an IND (Investigational New Drug) in 2013, then provided enforcement discretion exempting rCDI from the IND requirement. In 2023, it approved Rebyota (Ferring, live microbiota product, rectally administered) and Vowst (Seres Therapeutics, oral capsule) — the first FDA-approved microbiome therapies [309]. Non-commercial hospital FMT for rCDI may continue under enforcement discretion; non-CDI indications require a clinical trial protocol.
Canada: Health Canada regulates FMT as a biologic drug. Limited clinical application for rCDI is permitted without formal IND; commercial marketing requires full authorisation [313].
Europe – overview
The EMA's 2022 Horizon Scanning Report (EMA/204935/2022/Rev. 1, updated May 2025) states: "there is no agreed EU approach in relation to how FMT should be regulated" [263]. Member states apply three distinct frameworks — medicinal product, tissue/cell product, or therapeutic intervention. The report covers 18 countries and identifies August 2027 (SoHO Regulation 2024/1938 applicability) as the first binding harmonisation deadline.
Strict regulation – full medicinal product authorisation required
Germany: FMT is classified as a medicinal product (Arzneimittel) under the supervision of the Paul-Ehrlich-Institut. Outside clinical trials, full drug authorisation is mandatory. This is Europe's strictest FMT approach: non-profit donor banks cannot meet industrial GMP standards, so access is typically limited to clinical trial frameworks [263]. The AMG (Arzneimittelgesetz) contains no FMT-specific hospital exemption [263].
France: The ANSM (Agence Nationale de Sécurité du Médicament) classifies FMT as a special medicinal preparation (préparation spéciale), but authorises its use for rCDI in line with the Cammarota consensus and national guidelines. The Beaujon Hospital (Paris) donor bank is one of Europe's best. Although the legal category is medicinal product, a simplified hospital-equivalent pathway operates in practice for clinical use [263].
United Kingdom: The MHRA classifies FMT as a medicinal product for human application. The NHS authorises FMT for rCDI; clinical exceptions are available for accredited institutions. The Taymount Clinic and Guts UK (non-profit) provide private sector access. Since Brexit, UK regulation has developed independently from the EU SoHO framework [263].
Ireland: Classified as a medicinal product per the EMA table, under HPRA (Health Products Regulatory Authority) oversight. No detailed public protocol is available [263].
Czechia and Croatia: Both classify FMT as a medicinal product per the EMA table, under SÚKL (Czech) and HALMED (Croatian) oversight respectively. Access is typically limited to clinical trial frameworks [263].
Spain: Listed in the EMA table without a clearly assigned category. Based on available evidence, AEMPS (Agencia Española de Medicamentos y Productos Sanitarios) likely treats FMT as a medicinal product, which restricts clinical access — though FMT is actively researched in Spanish clinical trials [263].
Flexible regulation – tissue product or therapeutic intervention
Austria: The EMA table identifies Austria as applying Europe's most permissive FMT regulation [263]. Hospital-prepared, extemporaneous FMT is classified as a therapeutic intervention — not a drug, not a tissue product. This means hospital FMT carries virtually no drug authorisation obligation, only general clinical standards apply. Industrially manufactured FMT preparations, by contrast, fall under medicinal product regulation. This two-tier approach may serve as a model for SoHO Regulation implementation [263].
Denmark: Applies case-by-case classification — one of Europe's most pragmatic approaches according to the EMA [263]. FMT for dysbiosis treatment under hospital conditions may be regulated as a tissue product where processing is minimal (filtration, bag or capsule formulation). When an indication is explicitly claimed, FMT becomes a medicinal product. Any subpopulation of faecal material propagated as treatment is automatically a medicinal product. This flexible boundary allows hospital rCDI treatment to proceed with a relatively low administrative burden [263].
Netherlands: Listed in the EMA table; regulated as a tissue product in practice [263]. The Amsterdam UMC stool bank is one of Europe's most advanced donor bank models, with extensive donor screening protocols, and has become a reference point for European standardisation efforts. The Dutch approach demonstrates that clinical access and high quality assurance are achievable under tissue product classification [311], [316].
Belgium: EU Directive 2004/23/EC does not formally apply to FMT, but Belgium regulates it as a tissue product through national tissue and cells legislation — lower administrative burden than drug authorisation, while tissue bank quality assurance requirements apply [263].
Italy: Similarly regulated as a tissue product through national tissue law, despite Directive 2004/23/EC not formally applying. AIFA authorises clinical application for rCDI. The Fondazione Policlinico Gemelli donor bank represents an outstanding quality standard. Italy demonstrates that high donor safety standards are achievable within a tissue regulatory framework [263].
Sweden and Finland: Both listed in the EMA table without a clearly defined category. Based on Scandinavian regulatory culture and available literature, both likely treat FMT as a tissue product or flexible therapeutic intervention. In Finland, FMT for rCDI is actively researched in clinical trials; Fimea (Finnish Medicines Agency) has not published a known prohibitive position [263].
Portugal: Listed in the EMA table; detailed classification not publicly available. Clinical application appears limited and inconsistently regulated [263].
Hungary
Hungarian FMT regulation took a significant step forward in 2025: the Ministry of Interior published a new professional clinical guideline on 15 August 2025 on the performance of conventional intestinal microbiota transplantation procedures (identifier: 002338, validity: 3 years, until 15 August 2028). The guideline replaces the expired EMMI 002080 guideline (2020–2024), co-authored by the Gastroenterology and Hepatology Section (Prof. Dr. Áron Vincze) and the Infectology Section (Dr. János Szlávik) [314].
Key innovations of the new BM guideline: storage temperature revised to ≤ –70°C (max 12 months); thawing at room temperature required (warm water bath explicitly prohibited — Comamonas contamination risk); cryoprotectant (glycerol) use reconfirmed; terminology updated to "intestinal microbiota transplantation"; expanded indicative horizon: IBD (UC, Crohn's) mentioned, but not yet recommended for routine care [314].
The guideline remains a clinical professional document, not legal regulation. The legal classification of FMT in Hungary (drug, tissue product, or therapeutic intervention) remains unresolved. A uniform donor bank authorisation system, accreditation framework and mandatory registration are absent. Notably, Hungary does not even appear in the EMA table — domestic regulatory absence is thus documented not only nationally but at European level [263], [314]. MicroBiome Bank continues developing its quality assurance system based on the new BM guideline, and actively participates in the professional preparation of the SoHO Regulation's domestic implementation.
Asia and Oceania
Australia: The TGA regulates most FMT products as biologicals. Exception: where characterised strains are grown from established isolates with standardised consistency, such products may be regulated as medicines. rCDI clinical application is available through the Special Access Scheme [263].
China: National guidelines have regulated FMT since 2020. Donor selection and quality assurance protocols are detailed. The scope of indications is broader than in the West — IBD, IBS and metabolic syndrome are included [263].
Japan: Permitted within clinical trial frameworks; commercial application is limited. The PMDA adopts a cautious approach [263].
References
[263] EMA/HMA. Faecal Microbiota Transplantation – EU-IN Horizon Scanning Report. EMA/204935/2022/Rev. 1 (updated May 2025). 2022. Link
The 2022 (updated May 2025) EMA/HMA 'Faecal Microbiota Transplantation – EU-IN Horizon Scanning Report' (EMA/204935/2022/Rev. 1) is the official European Medicines Agency horizon-scanning analysis of FMT regulation. It maps the heterogeneous EU regulatory landscape (tissue, drug, blood-component or hybrid frameworks across member states), reviews clinical evidence by indication (CDI, IBD, hepatic encephalopathy, decolonisation of MDROs), and identifies harmonisation priorities. The report informs the EU SoHO Regulation 2024/1938 negotiations and proposes a coordinated approach to donor screening, stool-bank licensing, traceability, pharmacovigilance and clinical-trial registries. It is a key policy reference for EU FMT governance.
[309] FDA. Rebyota (fecal microbiota, live-jslm) approval. 2022. 2022. Link
This FDA news entry documents the 2022 approval of Rebyota (fecal microbiota, live-jslm) by Ferring Pharmaceuticals — the first FDA-approved fecal microbiota product. Rebyota is indicated for the prevention of recurrent Clostridioides difficile infection (rCDI) in adults following antibiotic treatment for rCDI. Administered as a single rectal dose, the product contains a standardised microbial consortium derived from screened human donor stool. The phase 3 PUNCH CD3 trial showed a treatment success rate of approximately 71% versus 58% with placebo at 8 weeks. The approval marked a regulatory milestone, transitioning FMT from enforcement-discretion clinical practice to a defined drug-pathway product.
[311] Keller JJ, Ooijevaar RE, Hvas CL et al. A standardised model for stool banking for faecal microbiota transplantation: a consensus report from a multidisciplinary UEG working group. United European Gastroenterol J. 2021. Link
This European consensus document provides detailed guidance on all processes related to collection, handling and clinical application of human donor stool for faecal microbiota transplantation (FMT). Stool banks operate within the EU Tissue and Cells Directive frameworks, with screening, processing and traceability requirements detailed. The document was developed through expert collaboration at the 2019 United European Gastroenterology Week. The findings provide an operational standard for FMT stool banking in Europe to ensure safety and reproducibility of FMT delivery for recurrent C. difficile infection and other indications.
[313] FDA. Enforcement Policy Regarding Investigational New Drug Requirements for Use of Fecal Microbiota for Transplantation. 2013. 2013. Link
The 2013 FDA 'Enforcement Policy Regarding Investigational New Drug Requirements for Use of Fecal Microbiota for Transplantation' (Guidance for Industry) established the agency's enforcement discretion for FMT use to treat C. difficile infection not responding to standard therapies, without requiring an Investigational New Drug (IND) application. The policy was a pragmatic response to clinical urgency, requiring informed consent and treatment by licensed providers, while reserving INDs for FMT used in other indications or settings. It has shaped the US FMT clinical landscape, enabling broad clinical access for rCDI while concentrating research-trial use under IND oversight. Updates and parallel FDA guidance have followed.
[314] Ministry of Interior (BM). Professional clinical guideline on conventional intestinal microbiota transplantation procedures. Identifier: 002338. Published: 15 August 2025. Valid until: 15 August 2028. (Replaces: EMMI 002080/2020.). 2025. Link
The 2025 Ministry of Interior (BM) of Hungary professional clinical guideline (Identifier 002338, published 15 August 2025, valid until 15 August 2028, replacing EMMI 002080/2020) on conventional intestinal microbiota transplantation procedures defines Hungarian standards for FMT practice. The document specifies donor screening, stool processing, storage and traceability requirements aligned with the EU SoHO Regulation; defines indications (primarily recurrent and refractory CDI, with research framework for other indications); specifies delivery routes (capsule, nasogastric/duodenal, colonoscopic, enema); and outlines pharmacovigilance, follow-up and registry obligations. The guideline is the operative national standard for hospital-based FMT services in Hungary and aligns domestic practice with European consensus.
[316] Cammarota G, Ianiro G, Kelly CR et al. International consensus conference on stool banking for faecal microbiota transplantation in clinical practice. Gut. 2019. Link
This international consensus from FMT experts in Europe, North America and Australia provides statements on stool banking for FMT, covering general principles, organization, donor selection and screening, stool collection/preparation/storage, services and clients, registries, outcome monitoring, ethics and FMT's evolving clinical role. Consensus was achieved through Delphi rounds plus plenary discussion, with statements supported by best available evidence. The document guides global stool-bank development to promote safe, equitable FMT access for recurrent C. difficile infection.