Zotero vs. EndNote

Two roller derby contestants

We here at ProfHacker are big fans of Zotero. Some of our earliest posts covered teaching with Zotero groups and making your WordPress blog Zotero-able (although we can’t control whether it’s “zo terrible” <rimshot>). And of course, there’s Amy’s fantastic two-part series on getting started with Zotero (parts one and two). The folks at the Roy Rosenzweig Center for History and New Media (who make Zotero) are friends of ProfHacker, and we got one of our earliest boosts from their Digital Campus podcast. That’s why I feel a little sheepish about making the following confession: while I admire and proselytize for Zotero, I actually use EndNote for my own research.

A few weeks ago, ProfHacker got a request asking us if we could compare the two platforms, which gave me a great opportunity to try to figure out why I prefer EndNote. In many ways, it comes down to the fact that I’m very, very comfortable with EndNote. I started playing around with it in my last year of undergraduate work (as a way to procrastinate rather than actually writing papers), and I purchased a copy of the software before starting graduate school (only to find out that my school had a site license). I fastidiously created bibliographic entries for the reading I did in seminars. I wrote abstracts for the articles. I learned how to create my own styles. I took library workshops on the tool. So when it came time to write my dissertation, EndNote was already well integrated into my workflow. I began experimenting with Zotero in the fall of 2007 (a year after its first release) and while I very much appreciated what it did, it wasn’t enough to make me a convert.

Apart from my own level of comfort, however, I wanted to know what the differences were between the two tools. In my postdoc I regularly teach classes on both EndNote and Zotero, which means that I think I’ve got a pretty good perspective on both tools. It must of course be said that both tools work very well at their primary purposes: managing references and creating citations and bibliographies within documents. With that, then, I want to cover what I see to be the strengths and key features of each platform. A couple of caveats: First, I’m not going to cover everything that each tool does. My goal is to just touch on some key differences that I’ve found for preferring one program over another. Second, while I’m doing my best to represent the features of both EndNote and Zotero, if I’ve missed something or gotten something just plain wrong, please let me know in the comments!

  • Cost: Perhaps the strongest selling point for Zotero is that it’s free. EndNote costs more than $100 for an educational license, and while in the grand scheme of things that might not be too much, it’s certainly an impediment for grad students or schools with limited resources. Winner? Zotero.
  • Collecting sources online: For many academic databases, library catalogs, and even sites like Amazon or The New York Times, adding a resource to your Zotero library simply takes a single click. It feels like magic the first time you do it, and it never stops feeling like magic. In response, EndNote created EndNote Web, which allows you install a bookmarklet to capture sources. It works across all browsers, but it’s nowhere near as robust nor does it capture information as well. Many academic databases allow you to export search results directly into EndNote, however. While it’s not quite as easy and simple as Zotero’s implementation, it works just as well and takes only a few seconds more. Winner? Zotero, by a hair.
  • Syncing: With Zotero 2.0, it became possible to keep your entire library in sync across all the computers you use. For many people, this is the most important feature, since it means you can do your work wherever you are, as long as you can install the Zotero plugin. EndNote Web is Thomson Reuters’s response; along with the bookmarklet, there’s an entire website where your sources are stored and which you can access wherever you have an Internet connection. The problem is that EndNote Web does not sync easily or well with your desktop library. So while you can create citations from either EndNote Web or EndNote proper, you can accidentally create differences between the two libraries. What’s more, I find EndNote Web to be slow and to have an unintuitive user interface. Zotero is just plain simpler for keeping everything together—plus since the Zotero library is stored locally, it’s accessible even when you’re not online. EndNote Web doesn’t do this. It’s worth mentioning that I’ve created my own solution for syncing my EndNote library: ProfHacker fave Dropbox. By storing my EndNote library files in Dropbox, they are kept in sync on all my computers and are stored locally. I just have to make sure that I exit the program on one computer before starting on another. Still, I have to give the edge to Zotero since its syncing solution is native to the application. Winner? Zotero.
  • Speed, overall: When I’m writing, flow is really important. Getting the thoughts down as quickly as they come is important, otherwise they’ll be long gone. Of course, I also need to cite things as I go, since figuring out what needs citations after the fact would be impossible. So the speed of the application I’m using matters a lot to me. When it comes to simply interacting with EndNote and Zotero, EndNote is just plain faster. Being a stand-alone application rather than based in Firefox—even Firefox 4 (see Amy’s quick review)—means that EndNote doesn’t have to depend on other things. Zotero Standalone is a possible solution (and Mark’s review praises it), but for now…Winner? EndNote.
  • Speed, inserting citations: Getting citations added into your document is a big part of the speed of using a tool. Both EndNote and Zotero have shortcut keys for inserting citations. Zotero then opens a window which allows you to search for your source, control how it appears, and then inserts the citation. EndNote has a similar option to Find Citations, but it also has a shortcut key that inserts whatever reference you currently have selected in EndNote. By not having to go through a pop-up window, you can drop a citation into EndNote much faster than you can with Zotero. Winner? EndNote.
  • Speed, editing citations: Not all citation styles require the use of page numbers, but my primary one—MLA—does. When I choose to insert citations into a document with either Zotero or EndNote, then, I have to make sure that I add in page numbers. Zotero includes an option to add page numbers in its Find/Add Citation dialog. EndNote does not give you this option. It immediately inserts and formats the citation, and you have to right-click and choose to edit it to add a page number. When used conventionally, then, Zotero is faster for adding page numbers. However, I’ve already said that I hate the pop-up box. EndNote gives me the option of turning off instant formatting. The result is that it drops snippets of code into the document like this: {Breuer, 1955 #81}. It’s not as pretty, but it’s super easy to add page numbers to this code: adding an “@” symbol plus the page number(s) is all it takes, {Breuer, 1955 #81@27-31}. Upon finishing the document, EndNote will convert this code into citations. Admittedly, working with EndNote this way is a level of citation ninja-ery that you might avoid. But it allows me to add in citations and page numbers quickly while avoiding the pop-up box. Winner? Zotero, for standard users; EndNote for advanced users.
  • Sharing sources with others: It’s not uncommon for scholars to be protective of their sources while writing, but there comes a point at either pre- or post-publication where we want to share what we’ve discovered. Zotero makes it easy to share sources with its groups feature. Adding sources to the group library is as easy as dragging them from your library into the group folder. And since groups can be private or public, you can even make the sources visible online for people who don’t want to join a group. EndNote allows you to share sources with others through EndNote Web. You can organize your sources into groups and then share groups with different people. There is no option to share sources publicly, and you have to manually add users to share groups by email address. It’s not terribly difficult, but it’s not implemented as well as Zotero’s sharing options. Winner? Zotero.
  • Writing with others: While most of us most often do our writing by ourselves, there are projects that require you to collaborate with one or more coauthors. Managing bibliographies when working on the same document can be difficult. EndNote and Zotero have very different solutions. EndNote creates a “traveling library” (scroll down after the link) embedded in each Word document that contains all of your collaborator’s bibliographic data and that can be imported into your own library. In other words, the bibliography and citations can be formatted correctly even if you don’t have access to the original records. Zotero’s groups, on the other hand, allows you to cite from your group libraries and it’s as easy as citing any other source with Zotero. Since I haven’t actually done a large project using either tool, I’m going to resist declaring a winner here.
  • Finding Full Text for Your Sources: EndNote and Zotero can both help you manage your PDFs as well as your citations. You can attach PDFs to source records, and the files then live in your library. However, when you create records, you often do not have the PDFs at hand. Zotero has a setting that directs it to “automatically attach associated PDFs and other files when saving items,” which always makes me think that it will download PDFs for me when saving sources from databases. Since it never does this, I’m quite sure that I misunderstand this setting; or perhaps it just doesn’t work with the databases I frequent. EndNote, on the other hand, has a built-in tool for finding full text versions of your sources. To have it work most effectively, you will need to configure it to go through your university’s database structure. But once you’ve done that and authenticated, it will scan your whole library to find either PDFs or URLs for your sources. In my highly non-scientific tests, EndNote finds full text for about 40% of the items I have in my library. It’s a whole lot better than downloading them yourself, although the process is pretty slow. Winner? EndNote.
  • Creating Sources from PDFs: On the other hand, sometimes you have a folder full of PDFs that you’ve collected and no metadata to go with them. Sure, you could enter that in by hand, but can Zotero or EndNote help you out here? Both applications have the ability to extract metadata from PDFs. For EndNote, you simply choose to Import, point it at a folder, and choose the “PDF File or Folder” import option. For Zotero, you can drag a PDF into your library, right-click, and choose “Retrieve metadata for PDF.” In my experience, EndNote has a hard time finding the metadata, but that very likely has to do with my field of study, since EndNote depends here on DOIs. Zotero, on the other hand, works with Google Scholar and gets better results for me. Aaron Tay, a librarian in Singapore, ran some tests onPDF metadata extraction for EndNote and Zotero (as well as two other reference managers)` and also found that Zotero came out on top. Winner? Zotero.
  • Customizability: Both Zotero and EndNote ship with most of what you need built-in, including the most-used styles and more fields for information than most people will ever need. If you find that you need to add a new type of source or some new fields for specific information that you need for your sources (unique identifiers for your project, etc.), EndNote is much better equipped to handle these needs: it has space for three new reference types and eight fields of custom information. Winner? EndNote.

To sum up, then, here are what I see as the different strengths of the two platforms:


  • Cost
  • Collecting sources online
  • Syncing
  • Speed, editing citations
  • Sharing with others
  • Creating sources from PDFs


  • Speed, overall
  • Speed, inserting citations
  • Speed, editing citations
  • Finding full text
  • Customizability

How you want to weigh those different strengths will affect which one you end up choosing to work with. Of course, the good news is that Zotero and EndNote play nice with each other. Since both support the RIS format, you can export sources (or a whole library) from EndNote and then import it into Zotero or vice versa. What this means is that you could use Zotero for collecting references and then use EndNote for actually composing documents. Or collect sources in EndNote and then share them with Zotero (which I’ve done with my dissertation library). Or any other combination that seems useful to you.

We know that there are plenty of other reference management tools. Ryan’s rounded up several when exploring how to organize and annotate PDFs and Julie covered Mendeley. But Zotero and EndNote are some of the biggest players in this space. Why do you prefer EndNote to Zotero or Zotero to EndNote? Let us know in the comments!

Lead image: Roller Derby: Convict City Rollers vs. The ‘Rat Pack. / Christopher Neugebauer / CC BY-SA 2.0

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