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Which reference manager?: Comparision of EndNote, Medeley and Zotero

This guide is intended to help you choose a right reference management tool for your study and research.

Reference management tools

A reference management tool is a software for storing and managing information resources. Generally, a reference management tool can help you:

  • import references from search engines, databases and websites 
  • save PDFs, images and other documents
  • annotate PDFs
  • insert citations and create bibliographies on Word documents  
  • collaborate with other researchers

EndNote, Mendeley and Zotero are the most popular reference management tools used by many researchers and students.

Find more details about these three tools in the following comparison table and detailed instructions in our online guides for each tool.

EndNote, Mendeley and Zotero: which is the best tool for you

The following comparison table of EndNote, Mendeley and Zotero may help you choose a right tool to meet your research needs.

Software support
  • AUT Library supports the use of EndNote (online guide, workshops and consultations)
  • Software support is provided by AUT ICT Services
  • EndNote website provides online training materials and a blog 
  • Mendeley website provides online training materials to support its users
  • Zotero website provides training materials and discussion forums/ blog for its users
  • Available in all AUT computers
  • AUT users can download a copy of this software free from the AUT website to a personal computer
  • Non- AUT members need to pay for using this software
  • Free
  • AUT holds Mendeley institutional membership. Use your AUT email to register your Mendeley account for more user benefits
  • Other option: free account for up to 2GB personal storage. Users can pay for extra online storage
  • Free for 300MB online storage 
  • Can pay for extra online storage
Operating systems
  • Windows 7, 8, 8.1, 10
  • MacOS 10.10 and above

Check the EndNote website for more details and latest updates.

  • Windows 7 (x64 and x86), Windows 8.1 (x64 and x86), Windows 10 (x64 and x86) 

  • MacOS 10.10 (Yosemite), MacOS 10.11 (EI Capitan)
  • Linux

Check the Mendeley website for more details and latest updates.

  • Windows: XP SP1 or later
  • MacOS: 10.9 or later
  • Linux

Check the Zotero website for more details and latest updates.


Online versions
  • Desktop
  • Online - EndNote Online
  • EndNote Online also provides a Matching publication feature that enable researchers to find the right journal for publishing
  • Free iPad app
  • Sync between devices
  • Desktop
  • Online - Mendeley Web
  • Mendeley web provides a database of publications. Researcher profiles available.
  • Free app for Android and MacOS. The iPad app has a better PDF reader.
  • Sync between devices
  • Desktop
  • Online
  • Third party apps. Don't recommend the use of these apps.
  • Sync between devices
  • An instant bibliography tool ZoteroBib is easy to create a bibliography and work with word documents
  • Unlimited local and online storage
  • AUT users: 100 GB personal storage & 100 GB shared storage
  • Free account: 2GB personal storage and 100 MB shared space
  • Unlimited local storage
  • 300MB free online storage
Work with Word processor
  • Desktop: MS Word, OpenOffice
  • EndNote cite while you write (CWYW) is a  comprehensive tool for citing resources and editing citations.
  • CWYW works with both EndNote desktop and Online versions
  • EndNote is a better tool for managing long documents and a large reference collection
  • MS Word, OpenOffice
  • Cite while you write with desktop library
  • MS Word, LibreOffice, Google Docs
  • Cite while you write with desktop library
Add references
  • Direct export references to EndNote from many databases
  • Import RIS, EndNote XML files
  • Drag and drop PDFs to a library and create references
  • Add references manually
  • Bookmark online resources to EndNote Online
  • Able to use "Find reference updates" to update references
  • EndNote desktop provides more options for managing references
  • Direct export from some databases
  • Import EndNote XML, RIS and BibTeX files from databases
  • Drag and drop PDFs to a library and create references
  • Use web Importer to get references from databases/websites instantly
  • Add references directly from Mendeley catalog
  • Add references manually
  • Direct export from a small number of databases
  • It is easier to use Zotero to collect references from websites. PDFs can also be downloaded along with reference data
  • Import RIS, BibTex, EndNote XML
  • Add references manually
  • Special feature: snapshots of webpages are also saved when adding references to the library
Save PDFs
  • Import PDFs or PDF folders
  • Automatically import PDF folders
  • Drag and drop PDFs to a library and create references
  • Use "Find full-text" to download PDFs with a DOI number
  • Limited PDF annotation function
  • Import PDFs using a Web importer
  • Drag and drop PDFs to a library and create references
  • Automatically import PDF folders
  • A better PDF annotation function than other two software
  • Use browser connector to collect references from websites. PDFs are sometimes downloaded along with reference data
  • Drag and drop PDFs/PDF folders to a library and create references
Edit output styles
  • Easy to edit output styles
  • A CSL editor is available
  • Use a CSL visual editor; It's not a easy process to modify a style
Share & collaborate
  • EndNote desktop library, including references, PDFs and annotation, can be shared with 100 people.  EndNote Online account is required for sharing the whole desktop library. 
  • EndNote Online - share groups of references
  • Personal research profile in Mendeley helps networking and provide opportunities for collaboration 
  • Can collaborate with up to 25 people
  • Share groups on Mendeley Web
  • Can share full-text in 1 private group only and with up to 3 people
  • Good for networking and collaborating
  • Can share citations and documents with others using your online account
  • As the size of a free Zotero account is only up to 300MB, sharing a large number of references/PDFs may need to pay for an extra data storage