My PhD thesis is manuscript-based, and I have 3 manuscripts (unpublished), included as 3 chapters into the thsis. The data analysis of my 3rd manuscript is mostly based on the results of the previous two (like my main independent variable in the 3rd manuscript is the result of my 1st manuscript).

Thus, when I write the methodology, I'm actually repeating a large portion of the methodologies from the previous manuscripts, and this is just too much for one manuscript. I'm thinking if in my thesis, I can say something like "the variable is generated from the analyses performed in previous study/chapter/manuscript", so I can save more space to the analyses of my 3rd manuscript.

  • 5
    This is a question you should ask your advisor. Commented May 13 at 1:35
  • What field are you in? In some areas of research, citing an unpublished manuscript is perfectly acceptable. Commented May 15 at 2:00

4 Answers 4


Think about this from the point of view of a reader or reviewer. The reader needs all this information for your research to be clear and reproducible. Your PhD thesis and your unpublished manuscripts will not normally be easily accessible to them. Also a reviewer may not want to look for such sources in order to assess your work. For essential information like this, you should therefore not cite these manuscripts. Many journals allow online supplements for their published papers, so if you have a large amount of information that is required for reproducibility but too long to have in the actual paper, put it in an online supplement. In the journals that I know, you'd submit the online supplement together with the main paper. Reviewers can then check this material, too.

You could get away, depending on journal guidelines (that sometimes allow such references and sometimes not), with certain references to your thesis such as "in some experiments we tried out this-or-that alternative approach but results weren't any good, see (...)". But not something that is of essential importance to the material presented in your actual main paper. (I have to qualify this by saying that there may be journals who'd even allow that, but I don't think it's good practice and chances are these journals are not so good.)

  • 3
    "Your PhD thesis and your unpublished manuscripts will not normally be easily accessible to them." That would depend a lot on where they got their doctorate. In Germany publishing your thesis is one of the basic requirements for getting your degree.
    – Maeher
    Commented May 13 at 10:08
  • @Maeher This doesn't necessarily mean that the thesis is then easily accessible to reviewers. Note that as a reviewer when it comes to specifics of research work that I'm expected to review, I generally don't want to be forced to look for cited literature, even if in a regular journal (of course there can be exceptions but what is explained here doesn't look like one). But fair enough, it may depend on country, field, and journal where they want to publish. Commented May 13 at 10:11
  • 15
    It's at least as easily accessible as any other published book. In practice many examination regulations nowadays allow the university library to act as the publisher, which means it is usually more easily accessible than your usual paywalled publication. I.e. they're freely accessible online, have assigned dois, and are indexed by the usual databases.
    – Maeher
    Commented May 13 at 10:20

PhD thesis is usually counted as a publication (and in principle is accessible from the relevant university library.) Thus, the usual practice would be simply citing the thesis. More over, it is equivalent to a publication in a refereed journal, as it was reviewed by experts (PhD committee or an equivalent) prior to awarding the PhD degree.

Another option is publishing the relevant materials online (e.g., on arXive) or making them available upon request - this has less weight as a publication, but provides the necessary information to those interested in understanding your work.


I would say that you can totally go ahead and refer to the other chapters of your thesis in your situation if you are willing and able to still change the third manuscript when you are actually going to publish it, if ever (and I don't really see why you wouldn't).

If so, when preparing your manuscript for submission to a journal, simply replace the relevant citations to either references:

  • to the published articles, if you have managed to publish them by then (best case scenario).
  • to your PhD thesis if you haven't.
  • a combination of the two if you were able to one article, but not the other.

In my reading, this is further acceptable, because referring to a different chapters is exactly how you would go about the problem if your thesis was not prepared in a "manuscript-based" style. And given that no part of your work has, in fact, been published yet, the style/format is really all that sets your thesis apart from a monograph-style thesis. And so I don't

The other answers given so far are flawed, in my opinion:

  • Roger V. advises to add a fully qualified citation to your thesis. However, at the time of writing you are not able to do so, because you probably don't know the exact DOI, volume, issue or even URL where your thesis will be available. And even if you were, some people might well regard citing your own work within the same work as an abusive form of self citation, as it will increase the citation count of said work. Roger V. also suggests that a PhD thesis is equivalent to a peer-reviewed journal article. I don't necessarily agree with that, because PhD theses are frequently reviewed only by members of the thesis committee, and it could be argued that there may be a conflict of interest, as is demonstrated by the much lower rejection rates of PhD thesis compared to journal article submissions (at least in the universities I know). Finally, at least at the time of drafting your thesis and adding the citations, your thesis hasn't been reviewed at all, so that argument doesn't even apply.
  • HEITZ doesn't explicitly recommend anything, but their answer implicitly could be read as advice not to reference to your other chapters because (1) readers of your work would not be able to find the information you are referencing, and (2) a citation implies peer review. Both are wrong, in my opinion. Given that your entire work is contained in the same volume (the PhD thesis/dissertation) and not published elsewhere, all information will be available to any reader (assuming that they have access to the entire work and not just the chapter or a page, but we would typically make that very same or even a stronger assumption for readers of a manuscript, who we also believe to have access to the entire manuscript, plus every other published article). And merely citing "citable resources" does not imply peer review, and neither should it. You can and should cite published works and resources that are not peer reviewed, such as preprints and datasets, as long as there is no better source available to refer to (e.g., prefer to cite a peer-reviewed article over its preprint, once available).
  • It appearst to me that Christian Hennig misunderstood the question (or perhaps I did?), understanding that you would like to publish manuscript 3, while not having published manuscripts 1 and 2 outside of your PhD thesis. But even if that were the case, I still think it is acceptable and not unusual to cite a PhD thesis as long as it is publicly available (as it usually is). In fact, I recently saw a case where an editor of a journal specifically asked to include a citation to a "manuscript-based" PhD thesis in a manuscript that included parts of the submitted work (though, in that case, the publication of the thesis was actually predated by publication in a preprint server, which was already cited).

Note, however, that Roger V. actually gives what is probably the best advice: Try to publish all of your articles on a preprint server like arXiv, or whatever is appropriate in your field. This not only avoids your problem (just publish manuscripts 1 and 2 first, then manuscript 3 after), but also gives your thesis the feel of a more conventional manuscript-based thesis. But of course, given your timelines, this may not be possible anymore at this point, as it would still probably take a week or up to a month before you get a citable identifier / DOI to include in manuscript 3. But maybe for next time :-D

  • _Try to publish all of your articles on a preprint server like arXiv, or whatever is appropriate in your field. _ <--- THIS Commented May 15 at 2:01

By referencing a work you are basically telling readers two things.

  1. where to find the referenced info. If readers cannot access referenced information due to unavailability or manuscript status, then you haven’t really provided the necessary info

  2. if it’s published, readers infer it’s been peer reviewed.

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