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EndNote desktop guide: Managing your references (EndNote X9)

Managing references

In this section we are going to look at the essentials of managing references in your library.

Reference / Preview / Attached PDFs tabs

In the top right corner of your library you will see three tabs; Reference, Preview and Attached PDFs

  • The Reference tab allows you to edit the various fields of a reference
  • The Preview tab allows you to preview the referencing style chosen
  • The PDF tab displays the full PDF document 

Reference/Preview/Attached tabs

Referencing style

You can select and preview your referencing style in the main window, using the drop down menu (see screenshot). A few styles will be offered initially and more are available if you click on 'Select Another Style'. The Preview tab on the right of the screen allows you to preview the style. If you wish to add a style that does not already available through the 'Select Another Style' option, e.g. BU Harvard, you will need to add it manually (see our guidance).

Reference styles screenshot

Editing a reference

To edit a reference, simply double click on the title of a reference and you will be presented with the editing screen. Click on a field to edit. Changes are auto saved generally but you can prompt a save by going File > Save, or you will be asked to save when you close the reference.

If you wish to edit a field but it does not appear, click on the gear wheel icon at the top right of the reference and toggle the Show Empty Fields / Hide Empty Fields option.

Screenshot of show hide empty fields option

Removing duplicates

Duplicates are very common in an EndNote library and it is essential that you remove them. The process is quite straight forward.

To screen references individually

  • Select,  References > Find duplicates
  • A dialogue box will appear, which shows the first of the duplicates and allows you to compare them. Ordinarily you delete the later added reference (see the refrence numbers in the screenshot below (green boxes)) as you may have already edited the existing reference

Screenshot of find duplicates dialogue box

The number of duplicates to review in indicated in the left pane

Screenshot of duplicate references folder


To remove all duplicates all in one go

There is a risk in removing them all in one go, as duplicate identification is not perfect, but it is a lot quicker than screening every reference


  • Select,  References > Find duplicates
  • A dialogue box will appear, which shows the first of the duplicates and allows you to compare them
  • Click cancel
  • The later reference for each set of duplicates will be highlighted in blue

Screenshot of duplicate references

  • Right click on any one of the blue highlighted references
  • Select move references to trash

Managing duplicate identification

You can manage how EndNote identifies duplicates through by going to

  • Edit > Preferences > Find duplicates
  • Use the check boxes to specify how EndNote identifies duplicates

Organising references in groups

Your references are categorised in the left pane of the library. 'All References' reflects all the references in your library. In the Groups section, you can create custom groups. There are three types of group, but the basic is the most useful.

  • To create a group, right click on My Groups, select Create Group, and give it a name
  • To populate a group, left click and hold on a reference in your library and drag and drop it to the group

Groups screenshots












Note: If you place a reference in a group, it does not remove that reference from All References, or create a copy of that reference. It is the same reference, with the same Record Number, just reflected in two places.

Note: If removing a reference from a group, make sure to choose the option to Remove Reference from Group, not Move Reference to Trash. If you remove to trash it will also remove it from All References.

Adding full text

Full text can be added for references, either by importing a file (usually a PDF) or by including a link to the full text online (not all full text is available as a file)

Adding a file e.g. PDF


  • Save the file you wish you attach to a reference, to your computer e.g. to your desktop
  • Open the reference you wish to attach it to (see edit reference for how to do this)
  • Identify the File attachment field
  • Drag and drop the file to this field


  • Highlight the references to which you wish to add the full text (it is often easiest to locate them to a group)
  • Click on the Find Full Text icon

Screenshot of find full text

  • EndNote will attempt retrieve full text files (where they are freely available or available through a University subscription). If a file cannot be retrieved, a URL to the full text will be inserted instead.
  • The results will be displayed in the panel on the left of your library
To set this up in your own purchased copy of EndNote please contact us


Import previously saved PDFs

To import a batch of PDFs previously saved to your computer see our section on Import locally saved PDFs

URL linking

Where a URL has been added to the URL field in a reference, either manually by yourself or automatically using Full Text Finder (see Harvesting above), highlight the reference and click on the Open Link icon to go to the full text online

Screenshot of open link