With the increasing use of electronic patient records, interoperability of patient-related data is of primary concern and international standards have been developed to assure compatibility between health data management systems. The present study is a first step in this direction for laboratory tests written in french, following the French government’s impetus for providing national health records for patients. To address the linguistic complexities inherent to this task, we adopt a natural language processing (NLP) methodology . Our pilot case study shows that computational linguistic assistance in aligning terminologies makes it 3 times faster for domain experts. The significant difference in performance between the existing state of the art and our tool reflects the impact of addressing the linguistic challenges involved in the mapping process, especially in the multilingual context.