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Usually institutes ask for three letters of reference for a postdoctoral position. Generically the first reference is the applicant's thesis adviser. Now my question is : does the ordering of second and third references matter? How should one choose the ordering?

For example, if an applicant is getting reference letters from a senior professor and a junior professor and he/she is quite sure that the junior prof. is going to give him/her a very strong letter. But he/she is not that sure about the strength of the other letter written by the senior prof. Who should he/she choose to be the 2nd reference?

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    But he/she is not that sure about the strength of the other letter written by the senior prof — Then he/she should either ask the senior prof directly whether their letter will be strong, or ask someone else for a letter. – JeffE Jun 10 '16 at 21:10
  • That's a great point! – Physics Moron Jun 10 '16 at 21:12
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In my experience I have never encountered a situation in which the ordering of reference letters mattered. Usually the only distinction between the different letters is when you are required to have letters from your PhD/postdoc supervisor. These letters may carry more weight because they are from the people which can best assess you.

However my experience is from life sciences, not physics.

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    "Usually the only distinction between the different letters... " - and even then, presumably it wouldn't matter if the supervisor's letter was attached to the application as Letter #1 or Letter #3, as long as it was there. (Unless the application has a separate place to put the supervisor's letter.) – ff524♦ Jun 10 '16 at 19:11
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    In physics (and I would assume all other fields, unless I am informed otherwise), the order of the letters does not matter at all. – Buzz Jun 10 '16 at 20:34

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