The clinical utility of transoesophageal echocardiography (TOE) is well established. Being a semi-invasive procedure, however, the potential for transmission of infection between sequential patients exists. This has implications for the protection of both patients and medical staff. Guidelines for disinfection during gastrointestinal endoscopy (GIE) have been in place for many years.(1,2) Unfortunately, similar guidance is lacking with respect to TOE. Although traversing the same body cavities and sharing many similarities with upper GIE, there are fundamental structural and procedural differences with TOE which merit special consideration in establishing a decontamination protocol. This document provides recommendations for TOE probe decontamination based on the available evidence, expert opinion, and modification of the current British Society of Gastroenterology guidelines.