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EndNote and EndNote Web: Exporting References from PubMed

Endnote:A Bibliographic Software Program; EndNote Web :Your Web-Based Research and Writing Tool

PubMed Import/Export

If your citations do not export properly into your EndNote library using the method in the adjacent column, please refer to the instructions below.

PubMed Import/Export Instructions


  • Go to the PubMed Database from the Loma Linda University Libraries' website. 
  • Put in your search terms and search the database for references.
  • Select citations you want to import into EndNote.
  • Under Send to menu, choose File.
  • Choose the Format as MEDLINE.
  • Choose Save File and click OK.
  • The citations will be saved as a text file and will be named pubmed_result.txt.


  • Open the EndNote Library in which you want the references to be incorporated.
  • Click on File, and then Import.
  • Click Choose File and find the txt. file that you had saved with your citations.
  • Select Filter, choose the PubMed (NLM) filter.
  • For Duplicates, you can either import all or discard duplicates.
  • Click Import.
  • The references are added to your All References group.
  • They are also temporarily in your PubMed (NLM) group under Online Search.

Exporting References from PubMed

  1. Conduct a search in PubMed.
  2. Check the boxes next to articles for the citations you wish to download.  If you're conducting multiple searches, save items to your Clipboard, a temporary storage space in PubMed.  You can do this by selecting Clipboard from the Send to menu.  If you do this, a Clipboard icon and the number of items on the Clipboard will be displayed at the upper right of the page.  To view the items on your Clipboard, click on the items link next to the Clipboard icon.

    Once you are ready to export your results, click the Send to menu at the upper right corner of your results or Clipboard.  Select Citation manager.  Then, click the Create File button. 

Mac Users: When working with EndNote on a Mac, you must use Mozilla Firefox as your browser to enable Direct Export (automatic downloads) of references from electronic databases (PubMed, Web of Science, etc.) to your EndNote library.

Send to Citation Manager

3.  A dialog box will appear prompting you to either "Open" or "Save" the text file that you are creating.

4. Choose the Open with radio button and select EndNote from the drop-down menu. If you do not see EndNote on the drop down shortlist, select Other and choose EndNote from the options provided. Then, click OK.

Open with EndNote X6

Your citations will automatically appear in your EndNote library.  If you do not already have EndNote open, your computer will open your EndNote library.