Trials registry records represent a challenge in deduplication compared to deduplicating studies reported in journals and exported from bibliographic databases such as MEDLINE. We demonstrate why this is the case and propose a method to deduplicate registry records from the WHO International Clinical Trials Registry Platform (ICTRP) and ClinicalTrials.gov (CTG) specifically in the reference management tool EndNote (desktop version). We believe that our method is not only more efficient but that it will minimise the risk of registry records being incorrectly removed as duplicates in automated deduplication. The method has seven steps and is detailed in this tutorial as a step-by-step guide.