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Reference management: Mendeley


Starting September 2022 Mendeley Desktop and Mendeley Desktop applications can no longer be installed!


Mendeley is a programme from Elsevier that can be used free of charge, but also has a paid Premium version (not in use at Utrecht University).
Mendeley helps you with collecting, organising, citing and sharing references to (often also full text) sources (articles, books, data etc.). 

If you want to start using Mendeley, install Mendeley Reference Manager.
This requires registration at Elsevier and downloading software. An Elsevier account includes all Elsevier products, such as Mendeley, Scopus and ScienceDirect.
Mendeley Reference Manager is available for Windows 7 or higher, Mac OS X 10-10 or higher, Linux and Ubuntu/Debian. 
Please note: Mendeley Reference Manager is not compatible with macOS 10.15.

Are you a long time Mendeley Desktop user?  Please note that as part of the continued evolution of Mendeley, from 1 September 2022, users will no longer be able to download and install Mendeley Desktop software. Existing users of Mendeley Desktop will continue to be able to sign into, use and sync their Mendeley Desktop.

Are you considering migrating to Reference Manager? Please visit the Mendeley Support Center.

Please note: Mendeley Reference Manager, so far, has no option for deduplicating!


Mendeley Support:


Mendeley Reference Manager 

NB Mendeley Desktop can no longer be installed, but if you already have it installed you can still use it (for the time being) 

Mendeley Reference Manager 

  • If you have not done so already, create a free account (NB: UU has no institutional account).
    • To avoid problems when logging in with Mendeley Desktop or Mendeley Reference Manager we advise you to create your account by using a private e-mail address and NOT your UU mail address.). If you have forgotten your password, click on 'Forgot password?' to reset.
  • UU-students:
  • Download and install Mendeley Reference Manager
  • Install if needed the Mendeley Web Importer (see above)) and the Citation plugin for Word (Mendeley Cite)
  • Next open Reference Manager here:
  • UU-staff:
  • Follow the explanation on UU intranet (under Reference Management).
  • UMCU staff:
    Via the UMCU IT helpdesk you can request permission to use EndNote. See UMCU intranet. Please note that the Mendeley Web Importer can not be downloaded within your browser on a UMCU desktop.
  • Install, if you want to, the Mendeley Web Importer (for Chrome, Microsoft Edge and Firefox) in your browser and drag/find the button in your bookmarks/favourites. This browser extension scans your current browser screen for references to articles and picks up possible metadata and full-text PDFs to add them to your library.
  • If you want to, also install the Citation plugin for Word (Mendeley Cite).

Get going:
In Mendeley Reference Manager choose under 'Collections' for 'New collection'.
Useful start page for MRM:

For further information, see:

Mendeley Desktop and Desktop applications can no longer be installed

Upgrade Mendeley Desktop library to Mendeley Reference manager
  1. Make sure your existing Mendeley Desktop library is synchronised
  2. Download and install Mendeley Reference Manager
  3. Log in with your Mendeley username and password and your existing library will be automatically synchronised

Tips & tricks

  • If you still use Mendeley Desktop you can (for the time being) use it at the same time with Mendeley Reference Manager. If you synchronise manually in Mendeley Desktop, all changes you have made will be automatically updated in Mendeley Reference Manager. And vice versa: all changes you have made in Mendeley Reference Manager will be automatically synchronised in the cloud and will show in Mendeley Desktop after you have carried out a manual synchronisation there.
  • On your telephone: download the free app for iOS or Android from your app store

Mendeley offers a number of options to collect references.

Mendeley Reference Manager
1. importing from another already existing collection (for instance from another reference tool);
. add files from your computer (drag & drop);
3. add manually)

mendeley add files

Extra option: the Mendeley Web Importer
Save references from the web directly to your Mendeley library with the Mendeley Web Importer. This browser extension scans your current browser window for references to articles and retrieves metadata and full-text PDFs where possible to add to your library.

Elsevier option: from a search system with Direct Export
From other Elsevier products, such as Scopus and ScienceDirect, you can import references in Mendeley via the Direct Export option 

  1. Log in at Mendeley before you start your search
  2. Select the title(s) from the list of results and click on Export. Next you choose the option Mendeley.

NB. Mendeley will not always find and add all data correctly, so always check your references. Improve and supplement them  with more data where necessary.

Mendeley Desktop
You can add documents to your Mendeley library by dragging and dropping a PDF into the Mendeley Desktop window. 
You can also use the File menu to Add files or manually create an entry.

Tips & tricks

  • Use the search field on and click on 'Add to library' to add the references you found. This tool supplements missing data, but works less well in the case of relatively unknown sources and may then add incorrect information or overwrite data! Always keep checking yourself! 
  • In Desktop you could use a DOI, PMID or ArXiv ID to collect data. Paste the identifier in the appropriate field and click on the magnifying glass icon.. The item will be searched for in the Mendeley Catalogue and will collect reference details available from other Mendeley users. If the reference is new, data will be collected from the owner of the identifier.
    Also in Reference Manager you can have data collected automatically in this way. Go to 'Add new', 'Add Manual Entry' and copy/paste the DOI in the field DOI field.
    Please note! The data can be incomplete or incorrect so always check the data yourself!

In Mendeley, you can organise your sources in several ways and add information to them. For instance, you can give your references a star so they are added to your 'Favorites' folder or mark them as (un)read. Or create folders yourself.
When you add a reference to a newly created folder/collection, you do not move it, but you give the reference a label. All your references are kept in the folder 'All References'. If you delete a folder/collection, the reference will remain available in 'All References'.

Mendeley Reference Manager
(manage existing collections and creating and searching new collections) 
(selecting, adding notes, highlighting, adding sticky notes, zooming in)

Please note:  If you want to modify the data of the reference, click on the title in question and next on the field to be modified under 'Info'.
edit authors in mendeley

In the PDF reader you can read documents (PDFs) and add notes to them:

  • In Reference Manager you click on the green tick under File. Or double-click on the title which both systems allow. The document opens in a separate tab. In Mendeley Desktop you open PDFs by clicking on the PDF icon.

    mendeley pdf reader

    In the PDF reader you can
    • Search in the text (use the search box on the right in the taskbar) The used search terms are highlighted in the text 
    • Highlight sections of the text
    • In Desktop: You can add notes about the entire document in the field 'General notes'
    • You can add 'Sticky notes' to specific sections in the text. In the text sticky notes are indicated by an icon. Click on the icon to read the note
      • In Reference Manager: to see all sticky notes in the PDF,  select the 'Info' button and choose the 'Annotations' tab
      • In Desktop: All notes can be viewed in the 'Notes' tab (next to the 'Details' tab in the right column)..
      • For more information about  'share, export, or print annotations', read this blog post.

Tips & tricks

  • In Reference Manager: use Mendeley Notebook to save highlights and notes from several PDFs in one place. You can open the notebook with the Notebook button above the PDF.

Mendeley Desktop
(use of filters, creating folders and subfolders, searching and adding tags)
(the PDF reader including the options: adding notes, highlighting texts, zooming in, synchronising)

Mendeley Reference Manager
In Mendeley Reference Manager there is no separate option for deduplicating.

Mendeley Desktop

  • Select in the left column the folder you want to deduplicate, this may be the folder 'All Documents', but also a folder you created yourself
  • Go to the Tools menu and select 'Check for Duplicates'
  • Now you see a list of duplicates
  • Click on the title you want to deduplicate to have a look at the underlying double references (select 'Details' in the right column)
  • Mendeley indicates which fields of the original titles have been chosen. You may adjust this by ticking or unticking the check box next to each field
  • Next click on 'Merge documents' to merge the references
  • You can also select 'Not a duplicate' to keep both the references
  • Repeat these steps for all your duplicates

Please note: Mendeley can automatically deduplicate titles when importing them without your knowing. You cannot switch off this function. This means you might lose references without you wanting to. That is why Mendeley is not suitable for creating systematic reviews.

For more information on deduplicating in Desktop see: 
or watch these videos:




For Mendeley Reference Manager: Mendeley Cite

Install Mendeley Cite for Word (and Libre Office).
For more information about Mendeley Cite see the help guide, for instance about:

NB. You can also use Mendeley Cite with Mendeley Desktop as long as you use a supported version of Microsoft Word and your Mendeley library is synchronised in the cloud.


For Mendeley Desktop: the Mendeley Citation Plugin
(need a citation tool: use Mendeley Cite)

It is no longer possible to install Desktop or Desktop applications.
If you still use Mendeley Citation Plugin, here is some information:

Open Word and click on the button References: there you will see a set of tools for Mendeley:

Mendeley Cite in Word

NB. At Libre Office of Microsoft Word for Mac it looks slightly different.

For more information about the Mendeley Citation Plugin see the help guide, for instance about:

Sharing documents and collaborating with others can be done in 'private groups'.  There is no limit to the number of private group members, but as a free user you may only create a maximum of five groups with a maximum of 25 participants.

You can add the full text of your PDF to the group so that everybody works in the same document. Everyone can highlight the text or add notes.

Private groups for Mendeley Reference Manager

Private groups for Desktop

N.B.: Some manuals still give information about Public Groups and invite-only groups. However, they have been cancelled as of April 2020.

Mendeley Reference Manager. Synchronising.

Mendeley Reference Manager saves all your references in the cloud (so not locally on your computer). If you are online, synchronisation is automatic and all modifications you made are saved. Hover with your mouse cursor over the sync icon to see when the most recent synchronisation took place and click on the icon to synchronise manually.

See also:

Please note! It is possible to add references manually off line in MRM. But make sure you regularly work online to synchronise with the cloud.

The offline use of Mendeley Reference Manager has some well-known problems. If you have problems, have a look here:


You can also export your references to a file. This file can be imported later (or in another programme).
Go to: Mendeley Desktop of: Mendeley Reference manager for instructions.

Mendeley Desktop

If you work online, Mendeley Desktop is fully synchronised with Mendeley Web. Your refererences are saved in the cloud. You can also synchronise manually by clicking on the Sync icon in Mendeley Desktop. Notes and annotations made in a group will then be available for other participants as well.
Please note! Your locally saved data may be of a  larger size than your free storage options in the cloud!

See also:

If you also regularly work off line or if you want to make sure that your library is safe in the case of an unexpected event, we recommend you to make regular backups of your Mendeley library. Also if you change accounts you must first make a backup. Go to the Help menu and click on Create Backup. Now you make a .zip file which you can save in a safe place on your computer.

Mendeley back up

To restore your backup, select Restore backup in the Help menu and next Other. Browse to your (most recent) saved zip file.

See also:

NB: You can use Mendeley Desktop at the same time with Mendeley Reference Manager. If you synchronise manually in Mendeley Desktop, all changes you have made will be automatically updated in Mendeley Reference Manager. And vice versa: all changes you have made in Mendeley Reference Manager will be automatically synchronised in the cloud and will show in Mendeley Desktop after you have carried out a manual synchronisation there.