Austria’s national Electronic Health Record (EHR) system holds information on medication prescriptions and dispenses in highly structured HL7 Clinical Document Architecture (CDA) documents. Making these data accessible for research is desirable due to their volume and completeness. This work describes our approach of transforming the HL7 CDA data into Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) and highlights a key challenge, namely mapping the Austrian drug terminology to OMOP standard concepts.