The goal of all clinical guidelines is to assist patients and practitioners in making healthcare decisions. However, clinical guidelines have been questioned about their quality, transparency and independence. Based on the revision of manuals by other scientific cardiothoracic organizations, this document provides instructions for the development of European Association for Cardio-Thoracic Surgery (EACTS) clinical guidelines and other types of evidence-based documents. Four key areas have been addressed: (i) selection of taskforce members and transparency of relations with the industry, (ii) methods for critical appraisal of medical evidence, (iii) rules for writing recommendations and (iv) review process. It is hoped that, by adopting this methodology, clinical guidelines produced by the EACTS will be well balanced, objective and, importantly, trusted by physicians and patients who benefit from their implementation.