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EndNote for Thesis Writers & Researchers

Working with Word, or Cite While You Write (CWYW)

For the basics of getting it right, check out the Inserting Citations to Create Bibliographies in Word in the Endnote X9 guide.

If you are considering using any software other than Word for your writing, check very carefully before you purchase it that it is fully EndNote - compatible. EndNote works with a range of Word processing programs; if you are unsure, check EndNote X9's compatibility requirements, or talk to us.

Some examples for the key areas where things have the potential to go wrong are:

Make sure that your EndNote library is in good shape with no duplicates and no incomplete or inaccurate references.

This is time-consuming and boring, but fixing the problems that arise from not doing it is far more time-consuming, extremely frustrating, and sometimes just plain scary. Make "first time right" your mantra.

Working with a long document means choosing between:

keeping the document as one file


breaking the work into chapters

working with Instant Formatting on


working with citations unformatted

linking to EndNote as you go


linking to EndNote only at the end

If you keep your document as a single Word file, and enter EndNote citations with the Instant Formatting turned on, you will find that the process becomes increasingly slow (really quite annoyingly slow) as EndNote reformats every single citation each time a new one is added.

Our strong recommendation is to have a separate Word document for each chapter, then it is an open choice as to whether you work with the following options:

  • Option 1 – Work with citations entered from EndNote using unformatted citations.
    If you are using an author-date style, you can, without the need to reformat,
    • exclude an author
      Durie states... {, 1998 #62}
    • exclude a year
      As early as 1998 it was established... {Durie, #62}
    • add a page range
      {Bishop, 2011 #51 @24-27}

    These will appear correctly formatted when you reformat at the end.

  • Option 2 – Work with the proposed citations noted in place with some sort of specific marker in Word, and connected to your EndNote library only at the end.
    This is preferred practice if you are working between desktop and online libraries.

    To do this, you would type in something like (+ Moyle 2014) where you want to insert that reference. Then it is easy at the end to search for instances of (+ to find where you want to insert specific references, then insert them from your EndNote library.

  • Option 3 – Work with citations entered from EndNote with the Instant Formatting on.
    When it comes time to put your chapters together, you will need to first convert the citations to unformatted in each of your chapters, then combine your chapters into one Word document, and then reformat (Update Citations and Bibliography in the EndNote toolbar).

If all the EndNote citations have been entered correctly and are all present in the accompanying library, then it is a fiddly, but relatively straightforward matter to put them all together into a single document at the end.

If you are unsure what you want to do, we are happy to discuss these options with you. For more information on putting your chapters together at the final stage, see our section on Combining Chapters.

EndNote uses code to create a link between the document you are writing and the EndNote library. This code needs to remain clear of other code, otherwise there is a risk it will be corrupted.

The most common code-dependent items that cause trouble are headings, tables, shapes and Track Changes annotations.

Make sure that any EndNote reference you have in your document is clear of these by at least one space, otherwise the citation could get corrupted (headings and Track Changes) or the inserted item fall to the end of the document (tables and shapes.)

Proceed carefully. If you think there may be a problem, e.g. you want to put a reference inside a table, you can test it by inserting just one reference, then saving the document. To check it, reopen the document and check that the table is still in place and/or the reference uncorrupted.

If this sounds risky, then contact us for help.

However carefully you have checked your records, errors may remain, and show up in your reference list to embarrass you. These errors must be corrected in your EndNote library, but you do not need to remove and re-insert the reference to do this.

  1. Highlight the in-text citation, whether it is author-date or numbered, and click on Edit Library References in the EndNote X9 toolbar in Word. This will take you to the correct reference in your EndNote library.
    EndNote - Correct reference from MS Word
  2. Correct the reference and save it.
  3. Back in Word, click on Update Citations and Bibliography to refresh the document.
    EndNote - Correct reference from MS Word

You may need or just want to change the referencing style of your document.

Traditionally author-date styles like APA 7th have a leading space before in-text citations, and numbered styles like Vancouver do not. When changing between these two very different types, EndNote does not adjust the placement of the in-text citation for you. Remember to allow for time to do this.

It is possible to amend EndNote referencing styles. Anything but simple changes (e.g. in-text numbers to superscript) is extremely fiddly work and liable to go badly wrong unless you rigorously test every change you make. This process is time-consuming, so always weigh the cost (your time) against the potential benefit before you start.

Make a time to see one of the Reference Team who can help you with the process.