A European consensus conference on faecal microbiota transplantation (FMT) in clinical practice was held to develop evidence-based recommendations for the implementation of FMT. The conference involved 28 experts from 10 countries, who collaborated in separate working groups to address key issues such as FMT indications, donor selection, preparation of faecal material, clinical management, and the establishment of FMT centres. The recommendations were developed through an electronic Delphi process and a plenary consensus conference, with statements evaluated and voted on by all members. The final recommendations were based on the best available evidence and aimed to guide physicians in implementing FMT, promote its broad availability, and support future research in gut microbiota manipulation. FMT is recommended as a treatment option for recurrent Clostridium difficile infection (rCDI), with high-quality evidence and strong recommendations. It is also considered for refractory CDI, although the evidence is lower. However, there is insufficient evidence to recommend FMT for the first episode of CDI. The consensus report also addresses other potential indications, such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), and metabolic disorders, but no evidence-based recommendations were made for these conditions. Donor selection involves a medical interview to exclude risk factors and a thorough screening process, including blood and stool testing. Donors should be healthy, with no history of infectious diseases or conditions that could compromise the safety of the procedure. The preparation of faecal material requires careful handling to ensure safety and efficacy, with both fresh and frozen faecal material being viable options. Clinical management and faecal delivery involve preparing recipients, selecting appropriate routes of administration (such as colonoscopy, enema, or upper GI tract), and ensuring safety during the procedure. The consensus report emphasizes the importance of monitoring patients for adverse events and efficacy outcomes, with follow-up recommended for at least 8 weeks after treatment. The establishment of FMT centres requires clinical expertise, appropriate facilities, and a multidisciplinary team including gastroenterologists, microbiologists, and infectious disease physicians. The centres must also have safe processing facilities for human samples and a clinical governance structure to manage administrative issues. The consensus report strongly recommends the implementation of FMT centres for the treatment of rCDI and outlines the technical, regulatory, administrative, and laboratory requirements for their establishment.A European consensus conference on faecal microbiota transplantation (FMT) in clinical practice was held to develop evidence-based recommendations for the implementation of FMT. The conference involved 28 experts from 10 countries, who collaborated in separate working groups to address key issues such as FMT indications, donor selection, preparation of faecal material, clinical management, and the establishment of FMT centres. The recommendations were developed through an electronic Delphi process and a plenary consensus conference, with statements evaluated and voted on by all members. The final recommendations were based on the best available evidence and aimed to guide physicians in implementing FMT, promote its broad availability, and support future research in gut microbiota manipulation. FMT is recommended as a treatment option for recurrent Clostridium difficile infection (rCDI), with high-quality evidence and strong recommendations. It is also considered for refractory CDI, although the evidence is lower. However, there is insufficient evidence to recommend FMT for the first episode of CDI. The consensus report also addresses other potential indications, such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), and metabolic disorders, but no evidence-based recommendations were made for these conditions. Donor selection involves a medical interview to exclude risk factors and a thorough screening process, including blood and stool testing. Donors should be healthy, with no history of infectious diseases or conditions that could compromise the safety of the procedure. The preparation of faecal material requires careful handling to ensure safety and efficacy, with both fresh and frozen faecal material being viable options. Clinical management and faecal delivery involve preparing recipients, selecting appropriate routes of administration (such as colonoscopy, enema, or upper GI tract), and ensuring safety during the procedure. The consensus report emphasizes the importance of monitoring patients for adverse events and efficacy outcomes, with follow-up recommended for at least 8 weeks after treatment. The establishment of FMT centres requires clinical expertise, appropriate facilities, and a multidisciplinary team including gastroenterologists, microbiologists, and infectious disease physicians. The centres must also have safe processing facilities for human samples and a clinical governance structure to manage administrative issues. The consensus report strongly recommends the implementation of FMT centres for the treatment of rCDI and outlines the technical, regulatory, administrative, and laboratory requirements for their establishment.