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Why do supervisors normally tell potential PhD students that they don't have funding, hence they can't accept students? does that mean the stipend? I thought stipend is paid through the department?

could someone clarify for me.

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Depending on your country, there may be different kinds of funding, including positions where you're an employee of the university/state/country. Such positions are usually owned by an individual professor. This is different from other funding sources that are not owned by individual professors, like stipends.

So, when you ask a professor if you can be her PhD student, without specifying a funding source, she may assume you're asking if she has a funded position readily available. In this situation, the answer is often no.

In addition, "no funding available" can also be a polite way of declining, if there are actually other reasons for saying no.

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    when you ask a professor if you can be her PhD student, without specifying a funding source, she may assume you're asking if she has a funded position readily available — Which is why you should always be explicit about whether you are asking for (a) advising, (b) funding, or (c) both. But beware that some faculty strongly prefer not to advise students that they are not funding, or to fund students that they are not advising. – JeffE Feb 5 '17 at 21:59
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Departmental stipends may not be enough, and are highly variable from one university to the next, and indeed from one department to the next. Hence, the specific reasons are highly variable. Moreover, such stipends may be paid through the department but might still come from a researcher's research grant(s).

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