Abstract Current societies undergo a transformation into information societies. “Digitialization” is progressing in every aspect of life, including health care. Handling the increasing flow of biomedical data presents a serious challenge to researchers and clinicians. Ontologies – controlled vocabularies that allow describing the meaning of data (its semantics) in a human and machine readable way are used more and more often to aid processing of information in biomedical research and in healthcare systems. The aim of this work is to bring closer the field of ontologies to the medical society. The theoretical basics are presented and exemplified with a range of ontologies used for describing diseases, medications, proteins, experimental procedures, etc. Currently the multitude of ontologies is an obstacle in further data integration. Unified Medical Language System (UMLS) and OBO Foundry (Open Biomedical Ontologies) are projects started to counteract this problem. UMLS aims at merging existing vocabularies, while OBO initiative is based on coordinated, harmonic development of new ontologies and reformation of existing ones. The pros and cons of both philosophies are presented. The final section of the article features examples of ontology applications.