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Mendeley: Organise

Learn how to use the reference management programme Mendeley.

Organising your Mendeley library

Add notes in PDF

You can highlight or add notes in a PDF document saved in your Mendeley.

  • In order to highlight a section in a document, you should select Highlight from the toolbar first.
  • To add a note, you should also select Note from the toolbar, then click a place where you want to add a note. A yellow box will pop up, type your notes in the box and close the box. A note icon will appear in the text.
  • You may Edit or Remove a note using a right click on the note icon.



Add notes in a reference record

  • Select a reference in the central column of your Mendeley library, then select Notes in the right column to add notes to this reference record.
  • For example, you could add a short summary of the article and how it relates to the context of your research. 


Using folders is a way of organizing your Mendeley library. Folders allow you to  group references together under headings of your choosing. You can store individual references in multiple folders. If you move a reference to a newly created folder it will appear in both the new folder and the All Documents folder (your main Mendeley library). 

Create a folder

  • Click Folders, enter a name for your folder.
  • Alternatively you can right click on the My Library heading and select New Folder
  • Once you have created a folder, you can create sub-folders within that folder, to further sub-divide your references. You can also rename folders at any time.

Add references to a folder

  • On All Documents (your main library), drag a reference into the newly created folder.


Delete a folder or a document in a folder

  • Highlight a folder or a document in a folder, then press the Delete button on your keyboard
  • References still remain in the All Documents folder. If you want to delete a reference completely from Mendeley, you should delete the reference from the All Documents folder. 

Rename Documents (PDF's etc.) 

Often, the PDF's or other documents you import into Mendeley will have arbitrary or meaningless file names, for example, a string of numbers or symbols, or a mixture of author names and numbers. 

The File Organizer function Mendeley allows you to rename the document stored in your Mendeley library, using the author/title/date/journal details that are present in the parent record of the document. 

To do this open your Mendeley, click on the Tools menu and select Options. File Organizer is one of the options. You should see a window that look like the below image: 

To rename your documents, tick the rename document files box. You can then choose which of the four file naming options you would like to choose to name your documents. Simply drag one (or several, or all) of the options (author/year/journal/title) from the Unused fields box to the File name box.

When you are finished, click Apply then OK. Mendeley will rename your documents. You can change the file names again later if you decide you would prefer a different document name format. 


The documents in your Mendeley library are stored in a specific location on your computer's hard drive. It is possible to use the File Organizer function organize these documents into subfolders within this location. To do this, use the Sort files into subfolders option in File Organizer. Your subfolder options are Year, Title, Author, Journal. 

Along with your desktop Mendeley, you can also create an online Mendeley account (see Mendeley Web tab). Once you have created an Mendeley Web account, you can use these sign in details to sign in to your Mendeley desktop.

This will allow you to save your desktop Mendeley library to your Mendeley Web account. This means you to access your library and documents from other computers. 

Automatic synchronization

If you are signed in to your Mendeley desktop, your references and documents should automatically synch with your Mendeley Web, to ensure your library remains consistent and current. 

To check whether the synch process is working correctly, add a document to your Mendeley desktop library. Press the synch button and wait for the document to synch. Log in to your Mendeley Web account and check whether the document has been added to your online library. 

Synchronization options

You might prefer to disable the automatic synchronization that is the default setting of Mendeley, for example if you have a limited internet connection. 

It is possible to adjust the automatic synchronisation from within your Mendeley desktop library, by right-clicking (Windows) on All Documents then Edit Settings

You can uncheck the synchronize attached files box. Be aware though that you will need to apply this change by clicking Save and Synch. Doing this will remove existing PDF's from your Mendeley Web. You can check the same box again later to reload them from your desktop Mendeley to Mendeley Web, but if you have large numbers of PDF's/attachments, then this process may be very time consuming. 

Another option might be to choose which folders you want to automatically synchronize, and which you don't by changing the synchronize process from entire library to selected folders. Only the folders that are checked will be synchronized. 


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