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The first British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS)-endorsed faecal microbiota transplant (FMT) guidelines were published in 2018. Over the past 5 years, there has been considerable growth in the evidence base (including publication of outcomes from large national FMT registries), necessitating an updated critical review of the literature and a second edition of the BSG/HIS FMT guidelines. These have been produced in accordance with National Institute for Health and Care Excellence-accredited methodology, thus have particular relevance for UK-based clinicians, but are intended to be of pertinence internationally. This second edition of the guidelines have been divided into recommendations, good practice points and recommendations against certain practices. With respect to FMT for Clostridioides difficile infection (CDI), key focus areas centred around timing of administration, increasing clinical experience of encapsulated FMT preparations and optimising donor screening. The latter topic is of particular relevance given the COVID-19 pandemic, and cases of patient morbidity and mortality resulting from FMT-related pathogen transmission. The guidelines also considered emergent literature on the use of FMT in non-CDI settings (including both gastrointestinal and non-gastrointestinal indications), reviewing relevant randomised controlled trials. Recommendations are provided regarding special areas (including compassionate FMT use), and considerations regarding the evolving landscape of FMT and microbiome therapeutics., Competing Interests: Competing interests: BHM has received consultation honoraria from Ferring Pharmaceuticals, Finch Therapeutics, Summit Therapeutics and speaker fees from Yakult. BMerrick received speaker fees from New Scientist. MNQ received speaker fees from BMS, Parapharm, Tillotts, Janssen and Takeda. NTE has received speaker fees from a company not related to the topic of this guideline. JPS received speaker fees from Takeda, AbbVie, Pfizer and BMS. NS received consultancy fees for advisory board for Pharmacosmos. ALH received fees for consultancy and speaker for AbbVie, Arena, Atlantic, Bristol-Myers Squibb, Celgene, Celltrion, Falk, Galapagos, Lilly, Janssen, MSD, Napp Pharmaceuticals, Pfizer, Pharmacosmos, Shire and Takeda; and also serves on the Global Steering Committee for Genentech. CS is a chair for the Healthcare Infection Society. JJK received consultancy fees from Vedanta Biosciences and Microviable Therapeutics and received a research grant from Vedanta Biosciences; and is a member of the scientific committee of European Helicobacter Microbiota Study group, member of the Scientific Advisory Board of 'Microviable Therapeutics', a member of a steering committee scientific study VE202 for ulcerative colitis (Vedanta Biosciences) and a founder and board member of Netherlands Donor Feces Bank (academic, non-profit). PH received consultancy and speaker fees from commercial companies and is a director of Modusmedica (since 2010 onwards). THI received consultancy fees from Ferring and speaker fees from Pharmacosmos and is a member of BSG/HIS microbiome for health expert panel and a director of University of Birmingham Microbiome Treatment Centre. SDG received consultancy honoraria from Enterobiotix and AstraZeneca, received speaker fees from Tillotts and has investments in biomedical company not related to the topic of this guideline. All other authors declared no conflicts of interest., (© Author(s) (or their employer(s)) 2024. No commercial re-use. See rights and permissions. Published by BMJ.)