EndNote Tip – Removing Duplicate Records while Maintaining Original Groups

If you’re using EndNote to keep track of unique numbers of articles (ie for a systematic review), you may run into issues if you have existing groups in your EN library.  Here is an example of how to properly de-duplicate records without messing up your original groups.  For more EndNote help, ask Peggy!  crusep@njhealth.org

Removing duplicates with groups

Let’s say you do a search on COPD and export 805 results into EndNote (line 2).  After removing duplicates in EndNote, you have 780 records.  Next, you want a subgroup of treatment articles so you limit your search accordingly (line 3).


You import the treatment articles into EndNote, put them in a Treatment group and remove duplicates within the Treatment group, which brings you down to 233 treatment articles.  There is no duplication within the Treatment group but all 233 records are duplicates from the original 780 imported articles.


To remove duplicates from All References and keep 233 treatment articles in the Treatment group:

  • Select All References in the navigation panel.


  • Go to References > Find Duplicates.
  • Select Cancel when the comparison window pops up.  This will close the comparison window and highlight the most recently imported duplicate records.


  • Drag all highlighted references to the Trash.  Your Treatment group now contains 0 articles, as these were the most recently imported records that you just moved to the trash.


  • A list of the 233 Treatment articles now exists in the select Duplicate References group in the navigation panel.  Select Duplicate References, highlight all records and drag them to the Treatment group.  You now have 780 unique records in All References, 233 of which are filed in the Treatment group.




7 thoughts on “EndNote Tip – Removing Duplicate Records while Maintaining Original Groups

    1. Yes, that’s true. When using this method, it’s critical that you remove duplicates within each batch after every import (see text above 2nd screenshot).

  1. Thank you so much for this guide! This allowed me to file the references of a finished manuscript into a custom group without having to select them all manually from my library or creating permanent duplicates after import of the references from the word file.

  2. Dear Peggy,

    Do you know about a way to find duplicates by comparing only the title names of the articles?
    I’ve imported about a thousand articles from PubMed and about 700 from PsycINFO. As for now, EndNote can’t find the duplicates since the way the authors are written differ just a little bit. Do I really have to go through them all manually?

    Thanks so much in advance,


    1. Hi Anton. Yes! You can change the de-duplication settings. Go to EndNote >> Preferences (on Mac), or Edit >> Preferences (on PC). Then select “Duplicates” in the left-hand menu. Un-check Author. Now, it will only look at the Title and Year field when comparing references.

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