SNOMED CT is a comprehensive controlled biomedical ontology widely used as an information exchange standard among various healthcare institutions. To ensure the unambiguous expression of health data and effective linguistic computation of word meanings, the hierarchical relation of a partially antonymous biomedical concept pair, which shares a common context but has antonymous modifiers such as in magnetic resonance imaging without contrast — magnetic resonance imaging with contrast, must be validated. This study examined the hierarchical matchings of partially antonymous concepts by the prepositional phrase without in SNOMED CT’s hierarchy. Among 132 and 477 partially antonymous pairs, 10 (7.6%) and 35 (7.3%) pairs were undesirably located under the Procedure and Disease hierarchies, respectively. Auditing efforts need to address partially antonymous concept pairs in SNOMED CT to provide a more reliable representation of semantic relations.