Clinical signs of gastrointestinal disease are amongst the most common presenting complaints in small animal veterinary practice. Over the last decade, many scientific advances have been made regarding determining the etiopathogenesis, improving diagnostics, and optimizing the treatment of various gastrointestinal diseases in dogs and cats. Despite this, there are still large knowledge gaps in our understanding of the underlying pathogenesis and, therefore, the development of non-invasive diagnostic methods or efficacious treatments for common gastrointestinal diseases, such as chronic inflammatory enteropathy, canine protein-losing enteropathy, and feline enteric-associated T-cell lymphoma-2. Therefore, the publication of new scientific findings focused on canine and feline gastroenterology will help to advance our understanding, diagnosis, and treatment of various gastrointestinal diseases. The aim of the present Special Issue was to gather, in one publication, the most recent advances in canine and feline gastrointestinal research.