Observing and reporting clinical signs in laboratory animals is necessary for many reasons: the assessment of animal welfare, compliance with the principle of refinement (e.g. humane endpoints), regulatory compliance (e.g. reporting severity) and, importantly, as a scientific outcome, e.g. in animal models of disease or safety studies. Developments in the reporting of clinical signs will enhance the scientific value gained from animal experiments and further address the ethical cost. This paper discusses systematic approaches to the observation and reporting of clinical signs in animals (to be) used for research. Glossaries from public and corporate institutions have been consulted and a reference glossary has been set up, providing terminology to be tailored for institutional or project-specific use. The clinical examination of animals must be carried out by competent and specifically trained staff in a systematic way and repeated at adequate intervals and clinical observations must be registered effectively to allow this information to be used. The development of institutional or project-specific glossaries and the use of handwritten records or automated databases are discussed in detail. Among the users are animal care staff, veterinarians and researchers who will need to agree on a given set of clinical signs to be monitored routinely or as a scientific read-out and to train for the proper application. The paper introduces a long list of clinical signs with scientific terminology, descriptions and explanations as a reference glossary to be published and maintained online as a living document supported by the authors as an editorial committee.