Fecal Microbiota Transplantation (FMT) is an emerging therapeutic approach in veterinary medicine, offering a promising solution for managing gastrointestinal disorders by restoring microbial diversity. This lecture provides veterinarians with a foundational understanding of the gut microbiome’s role in companion animal health, the mechanisms of FMT, and its clinical applications for such conditions as acute diarrhea, chronic enteropathies, antibiotic-associated dysbiosis, Canine Parvovirus, and Atopic Dermatitis. Attendees will learn about the different routes of administration, donor selection criteria, and safety considerations, ensuring responsible and effective implementation of FMT in practice. The session will also explore the future of microbiome-based therapies, including synthetic microbiota and next-generation probiotics. By the end of this lecture, veterinarians will have a comprehensive understanding of how to leverage FMT as a practical tool for improving patient outcomes.