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Abstract Background Data harmonisation is essential in real-world data (RWD) research projects based on hospital information systems databases, as coding systems differ between countries. The Hungarian hospital information systems and the national claims database use internationally known diagnosis codes, but data on medical procedures are recorded using national codes. There is no simple or standard solution for mapping the national codes to a standard coding system. Our aim was to map the Hungarian procedure codes (OENO) to SNOMED CT as part of the European Health Data Evidence Network (EHDEN) project. Methods We recruited 25 professionals from different specialties to manually map the procedure codes used between 2011 and 2021. A mapping protocol and training material were developed, results were regularly revised, and the challenges of mapping were recorded. Approximately 7% of the codes were mapped by more people in different specialties for validation purposes. Results We mapped 4661 OENO codes to standard vocabularies, mostly SNOMED CT. We categorized the challenges into three main areas: semantic, matching, and methodological. Semantic refers to the occasionally unclear meaning of the OENO codes, matching to the different granularity and purpose of the OENO and SNOMED CT vocabularies. Lastly, methodological challenges were used to describe issues related to the design of the above-mentioned two vocabularies. Conclusions The challenges and solutions presented here may help other researchers to design their process to map their national codes to standard vocabularies in order to achieve greater consistency in mapping results. Moreover, we believe that our work will allow for better use of RWD collected in Hungary in international research collaborations.