XVII. 3 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. On 30 November 2022 it approved Rebyota (Ferring, RBX2660, live microbiota product, rectally administered) [471], and on 26 April 2023 Vowst (Seres Therapeutics, SER-109, oral capsule) [472] – the first FDA-approved microbiome therapies [732]. 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.
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" [728]. Member states apply three distinct frameworks – medicinal product, tissue/cell product, or therapeutic intervention. The report covers 18 countries and identifies August 2027 as the first binding harmonisation deadline: Regulation (EU) 2024/1938 was adopted on 13 June 2024 and applies from 7 August 2027 [733].
Strict regulation – full medicinal product authorisation required
Germany: FMT is classified as a medicinal product (Arzneimittel) under the supervision of the Paul-Ehrlich-Institut [739]. 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 [728]. The AMG (Arzneimittelgesetz) contains no FMT-specific hospital exemption [728], [740].
France: The ANSM (Agence nationale de sécurité du médicament et des produits de santé) qualifies faecal microbiota as a medicinal product, on the ground that it is presented as having curative or preventive properties with regard to human disease. Outside clinical trials it may be produced under the magistral or hospital preparation regime (article L. 5121-1 of the French Public Health Code), and its preparation must take place under the responsibility of a hospital pharmacy (pharmacie à usage intérieur, PUI) [741]. The Beaujon Hospital (Paris) donor bank is one of Europe's best. The legal category is therefore the medicinal product, but the preparation regime gives clinical practice a workable route [728], [741].
United Kingdom: The MHRA (Medicines and Healthcare products Regulatory Agency) classifies FMT as a medicinal product for human use; centres that manufacture and supply FMT require an MHRA licence, while a pharmacy exemption may apply to named-patient supply within a single institution. For recurrent CDI, FMT is an accepted, guideline-recommended procedure within the NHS. Since Brexit, UK regulation has developed independently from the EU SoHO framework [777].
Ireland: Classified as a medicinal product per the EMA table, under HPRA (Health Products Regulatory Authority) oversight. No detailed public protocol is available [728].
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 [728].
Spain: Listed in the EMA table without a clearly assigned category [728], but the position was settled nationally in 2025: the joint consensus document of the ONT (Organización Nacional de Trasplantes) and the AEMPS (Agencia Española de Medicamentos y Productos Sanitarios), adopted on 21 May 2025 by the Transplant Commission of the Interterritorial Council of the National Health System, classifies FMT as a substance of human origin (SoHO) under Regulation (EU) 2024/1938. Registration, authorisation and inspection of establishments carrying out FMT fall to the ONT at national level and to the SoHO authorities designated by the autonomous communities at regional level [734].
Flexible regulation – tissue product or therapeutic intervention
Austria: The EMA table identifies Austria as applying Europe's most permissive FMT regulation [728]. 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 [728].
Denmark: Applies case-by-case classification – one of Europe's most pragmatic approaches according to the EMA [728]. 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 [728].
Netherlands: Listed in the EMA table; regulated as a tissue product in practice [728]. 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 [730], [735].
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 [728].
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 [728].
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 [728].
Portugal: Listed in the EMA table; detailed classification not publicly available. Clinical application appears limited and inconsistently regulated [728].
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) [736].
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 [736].
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 [728], [736]. 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 (Therapeutic Goods Administration) regulates most FMT products as biologicals; the mandatory minimum standards are set out in the 2020 TGO 105 determination. For indications beyond recurrent CDI, and for products not listed on the ARTG, use is possible within an approved clinical trial or through the Special Access Scheme.
China: Since 2020, a national expert consensus has set out the methodology of FMT (in China: washed microbiota transplantation, WMT): donor screening, the washing protocol, patient preparation, the delivery route, and safety requirements. The scope of indications is broader than in the West – IBD, IBS and metabolic syndrome are included [778].
Japan: Permitted within clinical trial frameworks; commercial application is limited. The PMDA adopts a cautious approach [728].
References
[471] . FDA Approves First Fecal Microbiota Product (Rebyota). . 2022. Link
FDA news release: on 30 November 2022 the U.S. FDA approved Rebyota (fecal microbiota, live-jslm; formerly RBX2660, Ferring/Rebiotix) — the first approved fecal microbiota product — for prevention of recurrent Clostridioides difficile infection (CDI) in adults (>=18 years) after completion of antibiotic treatment for recurrent CDI. It is administered rectally as a single dose.
[472] . FDA Approves First Orally Administered Fecal Microbiota Product (Vowst). . 2023. Link
FDA news release: in April 2023 the U.S. FDA approved Vowst (fecal microbiota spores, live-brpk; formerly SER-109, Seres Therapeutics) — the first orally administered fecal microbiota product — for prevention of recurrent CDI in adults after antibiotic treatment for recurrent CDI. Unlike rectally delivered Rebyota, Vowst is taken as oral capsules of purified bacterial spores.
[728] 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.
[730] 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.
[732] Nature Reviews Drug Discovery (news). FDA approves second microbiome-based C. difficile therapy. . 2023. Link
Nature Reviews Drug Discovery news summary on the FDA approval of the second microbiome-based C. difficile therapy: the April 26, 2023 authorization of Vowst (Seres Therapeutics, SER-109, oral spore capsule) – the first oral live-microbiota biotherapeutic for prevention of recurrent CDI – following the 2022 approval of the rectal Rebyota (Ferring, RBX2660). The article frames these two products as the first FDA-approved microbiome therapies and a milestone in FMT's transition to a regulated drug pathway.
[733] . Regulation (EU) 2024/1938 of the European Parliament and of the Council of 13 June 2024 on standards of quality and safety for substances of human origin intended for human application and repealing Directives 2002/98/EC and 2004/23/EC. Official Journal of the European Union, OJ L, 2024/1938, 17.7.2024. 2024. Link
Regulation (EU) 2024/1938 on substances of human origin (SoHO) was adopted on 13 June 2024 and published in the Official Journal on 17 July 2024, repealing Directive 2002/98/EC (blood) and Directive 2004/23/EC (tissues and cells). It entered into force on 6 August 2024, with the large majority of its provisions applying from 7 August 2027. Compared with the earlier directive framework, its scope is extended to further substances of human origin, including human breast milk and intestinal microbiota — the first binding European legal framework covering FMT.
[734] . Documento de consenso ONT-AEMPS sobre la donación, obtención, procesamiento y trasplante de microbiota fecal para el tratamiento de la infección por Clostridioides difficile. Organización Nacional de Trasplantes y Agencia Española de Medicamentos y Productos Sanitarios, Madrid. Versión final, 21 de mayo de 2025. 2025. Link
Joint consensus document of the Spanish National Transplant Organisation (ONT) and the Spanish Agency of Medicines and Medical Devices (AEMPS) on the donation, procurement, processing and transplantation of faecal microbiota for the treatment of Clostridioides difficile infection; final version, 21 May 2025, adopted by the Transplant Commission of the Interterritorial Council of the National Health System. The document classifies FMT as a substance of human origin (SoHO) under Regulation (EU) 2024/1938, designates the ONT as competent authority at national level and the SoHO authorities designated by the autonomous communities at regional level, and assigns to them the registration, authorisation and inspection of establishments carrying out FMT activities.
[735] 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.
[736] 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.
[739] . Substances of Human Origin: Paul-Ehrlich-Institut to Assume Central Roles Within the Framework of the SoHO Regulation. Paul-Ehrlich-Institut, Bundesinstitut für Impfstoffe und biomedizinische Arzneimittel, Langen. 2026. Link
Official Paul-Ehrlich-Institut (PEI) announcement that in Germany the PEI will act as the SoHO national authority and also as a SoHO competent authority, responsible for the authorisation of SoHO preparations, while the federal state authorities retain monitoring duties. The announcement explicitly notes that the scope of Regulation (EU) 2024/1938 is extended to further substances, namely human breast milk and intestinal microbiota. The Regulation entered into force on 6 August 2024 and becomes directly applicable on 7 August 2027 after a three-year implementation phase.
[740] Stallmach A, von Müller L, Storr M, Link A, Konturek PC, Solbach PC, Weiss KH, Wahler S, Vehreschild MJGT. Fäkaler Mikrobiota-Transfer (FMT) in Deutschland – Status und Perspektive. Zeitschrift für Gastroenterologie 62(4):490-499. 2024. Link
German expert review of the status and perspectives of faecal microbiota transfer (FMT) in Germany. It sets out that FMT in Germany qualifies as a medicinal product under the German Medicines Act (Arzneimittelgesetz, AMG) and describes the resulting authorisation and access consequences for clinical practice. The standard national reference for the German FMT regulatory situation.
[741] . La transplantation de microbiote fécal et son encadrement dans les essais cliniques. ANSM, Saint-Denis. Version de novembre 2016 (mise à jour de la version de juin 2015). 2016. Link
Framework document of the French National Agency for the Safety of Medicines and Health Products (ANSM) on faecal microbiota transplantation and its regulation in clinical trials; November 2016 version, updating the June 2015 version. The document establishes that faecal microbiota qualifies as a medicinal product under French law because it is presented as having curative or preventive properties with regard to human disease. Outside clinical trials it may be prepared as a magistral or hospital preparation (article L. 5121-1 of the French Public Health Code), and its preparation must take place under the responsibility of a hospital pharmacy (pharmacie à usage intérieur, PUI). The foundational document of French FMT regulation.
[777] Mullish BH, Merrick B, Quraishi MN et al. The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridioides difficile infection and other potential indications: second edition of joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines. Gut. 2024. Link
The 2024 second edition of the joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines on faecal microbiota transplant (FMT) for recurrent or refractory Clostridioides difficile infection and other potential indications. It updates the 2018 first edition with evidence from national FMT registries. It also sets out the UK regulatory framework: the MHRA treats FMT as a medicinal product for human use, centres processing and distributing FMT must obtain MHRA licences, and a pharmacy exemption may apply when FMT is supplied on a named-patient basis within a single organisation. Detailed recommendations cover donor screening, product manufacture, delivery routes and patient follow-up.
[778] Fecal Microbiota Transplantation-standardization Study Group. Nanjing consensus on methodology of washed microbiota transplantation. Chin Med J (Engl). 2020. Link
Chinese expert consensus on the methodology of washed microbiota transplantation (WMT), developed by 28 experts from 22 hospitals or institutes in 15 cities, organised into five working groups: donor screening, the microbiota washing protocol, patient preparation, choice of delivery route, and safety and adverse-event management. The document establishes an automated, machine-based washing procedure as the standard – distinct from manual FMT recommendations – and sets out quality-assurance requirements for Chinese practice. It is the most widely cited Chinese national-level FMT methodology guideline; the actual breadth of indications is documented separately in Chinese registry-based safety reports.