How to Use EndNote for Reference Management (A Comprehensive Guide)

What is EndNote?

EndNote is a referencing management software. It was designed for desktop use, both for Windows and Mac.

As a referencing software, EndNote streamlines your research process in the following ways:

  • Its inbuilt research tools allows you to search for relevant PDF resources that you can save in your account to use anytime.
  • Through cloud computing, you can access your research anywhere.
  • It simplifies your paper publication process by matching your research with relevant journals.
  • Allows collaboration with other researchers, regardless of geographical location. Not only can you share ideas and research resources among yourselves, your colleagues can also access your library materials through your permission.

How to Access EndNote

EndNote has been developed and maintained by Clarivate Analytics Company.

  • To use EndNote for desktop, access it through Clarivate’s website. Since it is a paid service, you have a 30-day free trial, after which you can choose to drop or purchase it.
  • Besides EndNote for desktop, there is EndNote Online, which is free to use, but only has basic, limited features. EndNote is compatible for both Windows and macOS operating systems.
  • After purchasing EndNote, register your software’s license. This keeps you on the loop in case of system updates and also guarantees product protection from the developer.
  • Create a free online account. Having an online EndNote account alongside the desktop software allows you to access your research anywhere, as long as there is an internet connection.
  • Register for EndNote training. Luckily, there are readily available training materials for mastering EndNote. In addition to training, online forums where users share their user experiences and queries are effective.

How to Create an EndNote Library

Here are simple steps to create your library:

  • Open EndNote. If accessing from your desktop, go to start> programs> EndNote. If accessing from a Word document, open the EndNote tab.
  • By default, EndNote opens your previous library. You can create a new one from the menu file> new.
  • Name and save your library.

How to Use Your EndNote Library

Your library is a collection of references that you can access anytime. How do you record references in EndNote? To generate and store references, either import or type manually. Here is how to do that:

How to manually type references

  • Go to references > new reference
  • From the drop down menu, choose your preferred reference type. The option Journal article appears by default. Other options include audiovisual, web page or book.
  • Select Output style (bibliographic style) from the main toolbar. There are thousands of styles to choose from, for example, APA, MLA, NLM, JAMA and Vancouver.
  • Use the numerous fields to put in relevant details. The fields include year, author, pages, titles, journal, volume and issue.
  • Use the research notes box to input any notes you may have about your references.
  • The advanced feature Term Lists automatically abbreviates journal titles. Nonetheless, you can abbreviate them based on your chosen Output style.
  • Create Author lists using any of the acceptable formats. EndNote also displays the list based on your Output style.
  • Follow your selected style guidelines when it comes to using capital letters on journal titles, books as well as articles.
  • As for text formatting, EndNote formats it as per Output style.
  • Upon completion, close the references. Go to File> Close Reference. It is automatically saved in your library.
  • Use the Tab Pane to preview your references.
  • Edit your references by double clicking on them in the library.

How to import references from online databases like PubMed

  • Search the database for the records you want to save.
  • Select the ones you want to save. In case you want to save all records from your search, leave them unmarked.
  • Click on the ‘Send To’ button. From the drop down list, you will see ‘Choose Destination’. Select ‘File’. Select your preferred format as well as sort by option. Click on ‘Create File’.
  • In the pop-up window, you will be prompted to either open or save the file. Click on ‘Save File’. Remember to note where the file is saved in your desktop.
  • Once done, go to your EndNote dashboard. Click ‘File’ from the home tab, go to ‘Import’ then ‘File’.
  • In the pop-up window, click the ‘Choose’ button to locate where your file is.
  • Open the file and select appropriate filter options.
  • Click on the ‘Import’ button and the references will be imported to your library.

How to export references from Google Scholar

You can export references from Google Scholar into EndNote online. To do this, first install the EndNote plug-in for internet explorer.

This allows direct export for Google Chrome, Microsoft Edge browser and Internet Explorer. It does not work for Firefox.

To use this plug-in,

  • Go to your EndNote ‘Help’ menu from the home tab. Select ‘Endnote online’.
  • You will be prompted to log in to your EndNote online account.
  • Open Google Scholar and go to ‘Options’ then ‘Settings’. This allows you to customize your downloads.
  • Set the Bibliography manager to ‘Show links to import citations into RefMan.
  • Your references will be imported into EndNote online and desktop. Save these changes.
  • Perform your search in Google Scholar. From the list of selected references, click on the ‘Import into RefMan’ option below each reference.
  • The subsequent steps will depend on your browser. In Chrome, you will see a drop-down arrow at the bottom-left. This allows you to ‘open this file’ or ‘always open files of this type’.
  • Choose a destination in which the references will be sent. Click on ‘EndNote Online’.
  • If you are already logged in to your EndNote online account, you will see the exported references in the ‘Unfiled’ group.

To import references to your desktop

  • Click on ‘Import into RefMan’. Open the files and select your destination as EndNote. Once you click ‘OK’, the references will appear on ‘Imported References’.
  • Most Google Scholar references miss certain metadata. Nonetheless, EndNote will find and update this information for you.

How to add Citations to a Word Document Using CWYW

If you have installed the Cite-While-You-Write (CWYW) plug-in for EndNote online, here are two ways you can insert citations to Word documents:

Method 1

  • On the Word document, place your cursor where the citation will be.
  • Click on the ‘Go to EndNote’ command. This takes you to EndNote where your library is displayed.
  • Select references to insert. For multiple references, hold down the control key while selecting.
  • Click on the ‘Insert Citation’ button from the toolbar.
  • You will be taken back to your Word document, where the references will be inserted.

Method 2

  • Use the ‘Insert Citation’ button on the top-left. When you click on it, a pop-up window appears. In the search box, enter your search words. EndNote brings a list of all records with the search words.
  • Select all relevant references and click the insert button at the bottom.
  • The references will appear in your Word document, with the formatted bibliography at the end of the paper.

How to Format Bibliographies

  • Use the ‘Configure Bibliography’ command. This arrow is on the bottom-right of the bibliography group.
  • In the pop-up window, you will be able to format your bibliography as you wish. You can change bibliography styles, hyperlink citations, font size, line spacing of citations or titles.

How to Remove In-Text Citations

  • Highlight the citation you want to remove. Go to ‘Edit and Manage Citation(s).
  • In the pop-up window, your selected reference will be highlighted in blue.
  • On the right, click the drop-down arrow labelled ‘Edit Reference’.
  • Select ‘Remove Citation’ and click ‘OK’.

How to Create Term Lists

Journal names may appear differently for similar references obtained from databases. For example, one journal may appear in abbreviation while another in full name.

Journal term lists are single phrases that come in handy when you want to search for the journals.

When setting journal term lists, ensure that you have configured your reference output style as well to match the term list.

To set term lists,

  • Go to ‘Tools’, select ‘Open Term List’, then ‘Journals Term List’.
  • In the pop-up window, you will see a list of journals. Delete this list.
  • Click on the ‘Lists’ tab and select the ‘Import List’ button.
  • Go to the ‘Terms’ folder either on the EndNote program folder in Windows or the EndNote application folder on Mac.
  • Select a journal list for the particular subject. Click the ‘Open’ button at the bottom.
  • You will be notified of the number of terms moved into the new journal list.
  • Click ‘OK’ then go to the ‘Terms’ tab. A list of journal names with matching abbreviations in suitable columns appears.

How to Organize Your References

Endnote allows you to group references together and remove duplicate citations.

To group references:

  • Use the ‘My Groups’ feature to create folders where you can group references as per topics, authors or even chapters.
  • Right-click on ‘My Group’ and select ‘Create Group’. A new folder will appear. Label it accordingly. Drag and drop all references you want in this folder.
  • Alternatively, use the ‘Create Smart Group’ option. This allows you to group references by specific fields. In the pop-up window, enter your desired criteria and click on ‘Create’. Endnote will display all references that fit these criteria.

To remove duplicate references:

  • Open the ‘All References’ section.
  • Click the ‘References’ tab from the toolbar. Select ‘Find Duplicates’. A pop-up window appears, prompting you to compare references. Choose the ones you want to keep. EndNote will delete the duplicates.

How to Publish Using Manuscript Matcher

Publish your work using EndNote’s Manuscript Matcher.

  • If using EndNote Online, click on the ‘Match’ tab. If using EndNote from your desktop, go to ‘My Groups’. Select a folder and right-click on it. Choose ‘Manuscript Matcher.
  • Open your work from a Word document. Click on the ‘Manuscript Matcher’ in the home tab to initiate the match-up process.
  • Copy the title and abstract of your paper onto the pop-up window that appears when you click on the ‘Match’ tab.
  • Click on the ‘Find Journals’ button.
  • Endnote will compare your information with thousands of journals within databases such as Web of Science.
  • If matches exist, a result of two to ten journals likely to be interested in your paper appears. You will also see a match score strength of your text with the listed journals.
  • Click on the ‘Submit to’ button on the right to begin your submission process.
  • Also, click on the ‘Journal Information’ button. This takes you to the journal homepage where you can learn more about it.

How to Share Your EndNote Library

To share your EndNote library, first synchronize it. This allows you to access from different devices.

  • Use the ‘Sync’ feature in your library to configure your desired library. To sync to another desktop, create a new library from the ‘File’ then ‘New’ command.
  • Once you have entered your EndNote credentials, go to ‘Library’ then ‘Sync’. The library contents will now be copied into the new library.

EndNote 20’s Library Sharing allows you to collaborate with fellow researchers. You can grant access to up to 100 users.

  • Go to File then Share. In the pop-up window, enter all email addresses of users. Here, you can also grant them permission to read contents or read and write.


Stay organized in your research process using EndNote. With its unique tools such as Cite-While-You-Write, your research is accelerated. EndNote is also functional both offline and online, hence you can work anywhere and still synchronize your work.

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Grace Njeri-Otieno

Grace Njeri-Otieno is a Kenyan, a wife, a mom, and currently a PhD student, among many other balls she juggles. She holds a Bachelors' and Masters' degrees in Economics and has more than 7 years' experience with an INGO. She was inspired to start this site so as to share the lessons learned throughout her PhD journey with other PhD students. Her vision for this site is "to become a go-to resource center for PhD students in all their spheres of learning."

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