Objectives: The Ontology of Bio-Medical Educational Objectives (OBEO) is a formal ontology for the annotation of educational objective catalogues and learning object resources to improve their usability. OBEO has been designed to allow semantic retrieval and navigation of educational objectives as well as the solution of questions in regard to consistency, sequence and correctness of educational objectives in databases. Methods: To specify OBEO various educational objective taxonomies and catalogues were analyzed and a requirements analysis was performed. OBEO was developed on the foundation of the top-level ontology Descriptive Ontology for Linguistic and Cognitive Engineering (DOLCE) and the upper-level ontology BioTop. It was implemented in the Web Ontology Language (OWL). Medical content is bound by links to reference terminologies and ontologies. Results: OBEO provides classes and relations for the correct and almost complete representation of educational objectives. OBEO formalizes the relations between educational objective specifications and the concrete actions which realize them as well as the medical contents which are bound to them. Although OBEO uses only few own classes and relations, its complexity is already extensive. Conclusion: OBEO is a prototypical tool to annotate existing and developing educational objective catalogues and learning object resources for their better usability. OBEO has to be further developed and improved in regard to the representation of medical content in educational objectives and the inclusion of curricular context of educational objectives. The formal representation of OBEO enables the retrieval and navigation of annotated data in regard to content.