Library Basics

  • When opening EndNote for the first time, you will need to create a new library. (File --> New)
  • You can rename it if you want, and then save it to your hard drive.
  • Don't save active EndNote libraries to a server or cloud-based storage, as they could corrupt over time. This includes OneDrive and iCloud, so make sure your libraries are not syncing to either service.
  • You can have as many libraries as you'd like, but if you plan to use EndNote online, you can only sync one desktop library to your online account.
  • You can customize the way your library looks. Under Edit --> Preferences, you can change the font under Display Fonts. Change which fields are shown in the library (author, title, rating, etc.) under Display Fields.
  • Need a backed up copy of your library? Create a compressed library (File--> Compressed library). Compressed libraries (with the file extension .enlx) can be stored anywhere, including in the cloud.

Adding References

There are 4 ways to add references to your EndNote library:


  • Select New Reference under the References tab, choose Reference Type (i.e. article, book) and type in the relevant info 

Search within EndNote

  • You can search some databases from directly within EndNote, and then add either everything you find or just selected references into your library. Click on the world icon (online search mode) in the EN toolbar, and click on the database you want to search. This is best for simple searches, like when you have a PubMed ID. 

Export from databases

  • Many databases allow you to export an EndNote or RIS file into EndNote
  • For example, in PubMed, go to Send to and select Citation Manager
  • Trying to add a book to your EndNote library? You can export reference information directly from PittCat

Import a text file

  • You can also import a text file, by selecting File -> Import
  • Select the appropriate import option (ex. EndNote import for EndNote files)

Organizing References

You can organize your EndNote library using groups. To create a group, go to Groups --> Create Group. Name it, and then drag and drop references into it.

There are other types of groups:

Smart Group

  • EndNote file references for you. Go to Groups --> Create Smart Group
  • Select the parameters for your group - what do you want in it? Articles by a certain author or on a certain subject? You can use Boolean operators (AND, OR, NOT) if needed.
  • EndNote will file all the references currently in your library that meet the criteria, as well as any future references you add

Combination Group

  • Create a group made from other groups. Go to Groups --> Create From Groups
  • Use Boolean operators to decide which articles from other groups should be in your new group

You can also create a Group Set, and file groups themselves by dragging and dropping

image showing groups and group sets in an EndNote library

Adding PDFs

When you add references, you're just getting the citation information. However, you can also attach PDFs, which can then be annotated inside EndNote.


  • Highlight the reference and click the paperclip in the right hand pane. You will be prompted to browse for the file. 

Have EndNote do the work

  • Select the reference(s) you're looking for, and then select References --> Find Full Text. EndNote will search for all freely available full text and attach PDFs it finds. You can ask EndNote to also search for articles Pitt subscribes to, which will bring back way more PDFs. To do that you need to add some information to your preferences; the instructions are located here: Full Text Set Up 
  • Note: EndNote won't find everything, but it will save you a lot of work

Have a PDF (or folder of PDFs...) and just want to quickly import it into EndNote as a reference?

  • File --> Import, then select file or folder
  • Browse for your file/folder
  • Select PDF as your import option (if you have a Mac, make sure you click on the options button to do this)
  • Double check your reference - if it is a scanned copy or doesn't have a DOI, it will not import properly

Annotating PDFs

You can easily annotate PDFs in EndNote. Double click any reference that has an attached PDF, and then click on the PDF. From there, underline, highlight, or add notes.

example of an annotated article, with highlighted and underlined passages

Finding retracted articles in your library

Sometimes articles may be retracted, corrected, or otherwise flagged after publication. EndNote does not have any mechanisms for alerting you if papers in your library have been retracted. EndNote also does not import this information when you initially download references into your library, so if you add a new reference you won't necessarily know if it has a potential issue. However, you can create a customized PubMed filter that will allow you to collect this additional information when you bring PubMed references into your library. (Note that if papers are retracted or corrected after you have imported them you will not be alerted, even if you used this filter.) The directions for creating a PubMed filter are below:

EndNote + Zotero

The citation manager Zotero alerts users to retractions via an integration with Retraction Watch. EndNote users can use the two citation managers together to check for retractions. To do this, download and install the Zotero software. When you're ready to check for retractions, export your EndNote references as an ris file and then import that file into Zotero. If you have any retracted references in your file Zotero will immediately alert you.