BACKGROUND: SNOMED CT is the most comprehensive medical terminology. However, its use for intelligent services based on formal reasoning is questionable. METHODS: The analysis of the structure of SNOMED CT is based on the formal top-level ontology DOLCE. RESULTS: The analysis revealed several ontological and knowledge-engineering errors, the most important are errors in the hierarchy (mostly from an ontological point of view, but also regarding medical aspects) and the mixing of subsumption relations with other types (mostly 'part of'). CONCLUSION: The found errors impede formal reasoning. The paper presents a possible way to correct these problems.