Discarding duplicates while downloading
Do not choose this option. Remove duplicates afterwards so you can check if they are real duplicates.
Check via Preferences (Top bar > Edit > Preferences > Duplicates) the criteria for deduplicating. The default settings are 'author, year, title'. Add Journal name or 'DOI' to discard real duplicates.
Duplicates removal after import
The searching for duplicates method is safest, but requires more work.
Method: Top bar > Library > Find duplicates
Each duplicate will be presented in a window. You can judge whether it is a true duplicate record or not. Sometimes references from the same article differ in how they are presented. Sometimes they are incomplete. In that case always keep the more complete reference.
See also:
EndNote 2025/21/20: Steps to remove duplicates from your EndNote library
Another fast and effective deduplication tool (not from Endnote.com) is DedupEndnote.
DedupEndNote is a tool for removing duplicate records from EndNote or Zotero databases exported in RIS format. It is more flexible than the built in deduplication features in EndNote or Zotero, and identifies a lot more duplicates than those programs.
If you use this software, please cite it as:
Lobbestael, G. (2025). DedupEndNote (Version 1.1.0) [Computer software]. https://github.com/globbestael/DedupEndNote