Impact of gap year during phd program on future post-doc and employment options? I am a Doctoral candidate in a top program in my field in the U.S. I should be starting my second year of classes in September before sitting for qualifying exams, however I had an catastrophic academic year. My program Chair and Dean of Students are have been understanding on my situation and have offered me all the support possible to allow me to resolve the issues that got in the way. Provided this, they  have recommended I take a medical leave of absence from my program to I would start fresh.  The way things currently stand, my transcript shows okay grades for the Fall semester and failing grades for the spring. I have asked for a retroactive medical leave that would wipe my slate clean, at least  for the spring semester. This may or may not be possible to do.  In the event that I can't wipe my failing grades from the spring semester record and return to complete my program with an outstanding record, I wonder if and how having a gap year will on my transcript affect my candidacy when applying for top-notch post-doc positions and fellowships?
It is not uncommon to have a break doing a PhD program, especially in the U.S. where it normally takes longer than in other countries. A list of reasons to have a gap includes maternity, health conditions, family situations (in some countries / cultures), or even temporary financial reasons. All these explanations seem fair to me, and I would not hold such them against the candidate.

What is very important, though, is


how (and whether) you will address the gap in your cover letter 
how your supervisor will speak about this in the recommendation letter.


If you are open to your colleagues and do not let them down without a reason (in other words, if you are doing your best given the situation), I do not see why the situation itself should be held against you and diminish your chances of future success.