Strictly speaking, this is not a LaTeX question. However, I suspect it will be very interesting to LaTeX users.

What are the advantages of using a commercial reference management system like EndNote over using BibTex? I suspect the primary reason people use EndNote is because they are using Word and Word doesn't support BibTex. Are there any other reasons to use EndNote instead of or in conjunction with BibTex?

I ask this because systems like EndNote strike me as something that I would have to use a fair amount to understand the relative advantages. I would prefer that only individuals who have significant experience with both EndNote and BibTex answer this.

My field is computer science, and BibTex is usually not too hard to come by in computer science. However, some bibliography services support EndNote but not Bibtex.

8 Answers 8


I don't use Endnote, but I frequently edit Word documents whose bibliographies have been prepared using it. The following contains much extrapolation from personal impressions.

They have different ideas about use. Endnote is a bit more like Zotero than traditional Bibtex, stressing its access to official abstract and bibliography servers, with many users who have never either edited a bibliography entry themselves, or felt that they are maintainers of a bibliographic database, because they haven't felt the need. The idea is that that the professionals have taken care of the massive Endnote bibliographic database, so that you don't have to worry about it. This idea of being taken care of is supported by the work that the Endnote producers (recently Endnote was acquired by Thomson-Reuters, now one of the world's two giant news & professional information agencies) have put into cultivating a dialog with the major style guides, such as APA, so that their output is accepted by the authority as being in conformance with the official style.

The results are pretty good, but not as good as users expect. Very commonly I received manuscripts from clients who say I don't need to look at the bibliography because it was prepared with Endnote. I then look over the bibliography to see if I find any errors. Inevitably I do, occasionally serious ones, which I report back to the sometimes very surprised client.

Endnote allows export to Bibtex format. If you do so, the promises about conformance to style guides become worthless, as the Endnote representation of reference metadata does not cleanly correspond to Bibtex's. I have the idea that the same problems will apply if one tries to convert Endnote's format into the new Word 2010 reference format, but I have not confirmed this.

Bibtex is free. The standard Endnote package has an RRP of $300, and will require fairly frequent paid upgrades for most of its users.

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    +1 for mentioning Zotero. I do think Zotero versus EndNote is a much fairer comparison in terms of features and goals. And one anecdote: my wife showed Zotero to her PI, who had been using EndNote for the better part of the past decade. The lab made the switch within two months, so Zotero is at least doing something right. I think the biggest complaint they had with EndNote is that every now and then, adding and removing references completely screw up the citation-mark numbers in text. (I'm not sure if the problem was between keyboard and chair or not.) Dec 9, 2010 at 11:39
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    @Willie: Zotero is doing enough right that they are now being sued by Thomson-Reuters. What document preparation software was your wife's lab using? Dec 9, 2010 at 12:20
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    ... Microsoft Word ... (for them, collaborative editing is a must) Dec 9, 2010 at 17:31
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    I am aware of several people that had their entire endnode databases get corrupted midway through PhD. This sort of thing will virtually never happen with bibtex. Nov 6, 2016 at 3:32

I've had some issues with EndNote over the years, some of which have been addressed in more recent releases or perhaps 'go away' if you switch from .doc to .docx Word files. My boss wrote a paper about 18 months ago with a large EndNote library and sent it to another academic for some editing. This all worked fined until my boss wanted to alter the references a bit. Our colleague uses OpenOffice, and although it preserved the look of the references it lost the library element. So they all had to be re-done by hand. As I say, that was a document in .doc format, and we might have been better in the more open .docx format.

I've successfully used BibTeX4Word in the past, as it lets you use a BibTeX database and style file with Word (provided you are reasonably careful). For me that's always been a good balance: I have to use Word at work, but prefer to have my references in BibTeX format.

Charles is quite right that the big selling point for EndNote is the idea that the user doesn't have to worry about the 'bibliography management' side of things. However, I'd also agree with Charles that this doesn't quite work out as you'd like. At least in my field (chemistry) we reference stuff that is in press or has complex notes to add to the references. Nothing automated is that good for these, so whatever approach is uses there is still a lot of typing to do.


Endnote is still the standard in several fields and some people are forced to use it because they have to collaborate with other Endnote users. Still, my advice is: If you don't have to use it, stay away from it.

Endnote is a buggy and overpriced piece of crap with serious limitations. I haven't used Endnote for quite some time and just downloaded the latest trial to have a look at it, and guess what: It still has the style editor it had 15 year ago; if you're in English speaking hard sciences, this will probably do, but anything a bit more advanced is a problem. Modern systems like CSL (Zotero et al.) or biblatex are incredibly more powerful.

Many of Endnote's shortcomings have been known for year, but Thomson Reuter's support boils down to a regular $99 bug fix release.

Oh, and it looks like its BibTeX exporter is still broken by default.


It is much easier to write an automated script to process an EndNote file than a BibTeX file. BibTeX has nested braces serving different roles depending on the level of nesting:

{author} = {Bj{\o}rn},

EndNote does not:

%A Bj{\o}rn


In my field, i.e. Ancient Philosophy, EndNote looks like the only choice: BibTex presupposes that the main address field looks more or less the same in all bibliographic styles and, because of that, uses much less database fields. EndNote allows me to play with issues like multiple editors, authors, series vs book editors, or source text editions made in the same book by a different author than the one who did translation and the other one, who did the commentary. I re-define the styles included with EndNote, as they contain too many errors. Actually, I am looking for a method to use directly my Endnote databases in Latex, i.e. without Bibtech, but I cannot find any efficient solution.


I have tried both Endnote and Mendeley in handling my bibtex file. Mendeley, which is free, seems superior to Endnote for several reasons;

  • Mendeley directly converts the mendeley bibliography to a bibtex, and when you press sync it automatically updates the bibtex-file. The only problem is handling letters like æ, ø, å, which disappear if you do not go through the bibtex-file by yourself. In the support site of Mendeley it seems that they are eagerly trying to make Mendeley better at formatting the output for bibtex and bib latex. http://blog.mendeley.com/tipstricks/howto-use-mendeley-to-create-citations-using-latex-and-bibtex/

  • Endnote is way more tedious to use for handling the Bibtex-file. It exports the endnote-bibliography to a bibtex-file just fine, but will not be able to synchronize as easily as mendeley.

I myself prefer to use a bibliography-management program to prepare all the citations - it saves me a lot of time!

Good luck!

  • mendeley is the controversy after being acquired by elsevier. so it's not rainbows all the way.
    – percusse
    Nov 5, 2013 at 14:41
  • #percusse I read that they will keep it free. But who knows - let's cross whatever is crossable.
    – Khaurum
    Nov 7, 2013 at 8:01

In my experience, Endnote can be used with relatively good success with newer versions of Microsoft Office (whe then already have two proprietary pieces of software), but it can cause havoc when trying to format documents. Usually it works without trouble and introduces the citations as needed. I use the program through an institutional licence (otherwise it would be too expensive) and it comes quite handy here - especially in the life science field. Here I can either get the citations from the journal websites or through PubMed without hassle. And it can export BibTex libraries, that can be used by BibLatex without problems. I set a label into the label field of Endnote, which can then be used as a cite key by BibLatex.


I have authored documents using both Zotero and EndNote. I write some of my larger analyses using RMarkdown (which uses LaTEX markup). Here's my 2 cents on the topic.

Why EndNote is better?

Cite While you write in Word is a very nice feature for a lot of people I work with. For me the greatest feature is being able to search for an article in their "browser" tab. You can then add it to a collection. So far Zotero does all of this. Where EndNote is different is that I can automatically download the PDFs and rename them according to a predetermined syntax. This might seem trivial but if you are going to be doing a large literature review you are easily saving 1/2 the time


If you do decide to use RMarkdown there is the citr package which allows you to dynamically add BibTex references while you code which is great. While I am writing I know which article I'm looking for but rarely will I remember the bibtex reference (I mean who does).

The workaround

I admit this is not the greatest way but since Zotero does not, to my knowledge, allow for automatic downloads I will probably continue to use Endnote to organize and download my references. I can then export to Zotero or a BibTex file to write my document.

Hope this helps!

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