Can late recommendation letters have a negative impact on grad school application? I am currently applying to some graduate programs. The schools I am applying to have all required recommendation letters from 3 people, and for many of the schools, the application deadline was today. Two of my professors have submitted their recommendation letters on time, but the last one - not being the epitome of a very organized person, sadly - has failed to meet the deadline. (Changing this recommender does not come into question, because she is my advisor, and she happens to be more familiar with me and my work than any other professor. Also, I cannot really ask anyone else to write a recommendation letter for me within such a narrow timeframe.) 

This raises two questions for me: First, is the electronic system for submitting recommendation letters kept open beyond the deadline so that late recommendation letters can be received? (I understand that different schools may have different policies, but it would be relieving for me to know that my professor still has a chance to submit her recommendation. So I'd appreciate it if someone could inform me what the norm is in such cases. Before you ask, yes, I will e-mail the graduate admissions offices of the schools in question, too. But I do not think I can get a quick reply, as they are usually inundated with e-mails during the application season.) 

Secondly, and more importantly, would the lateness of this recommendation leave a bad impression on the admissions committee?
Sometimes the deadlines for recommendations are flexible, and the references have some grace time to get them in.  In my department, we are certainly flexible, but we are not exactly inundated with well qualified applicants either.  I think our approach is pretty typical (at least for the sciences and engineering).  However, I have heard of higher ranked schools being more of sticklers for about the deadlines.

However, if the letter is accepted, then when it happened to arrive is totally irrelevant.  The faculty evaluating the applications almost certainly don't even see when the various parts of the application file arrived.  And even if somebody did see that a letter was late, if anyone were to be blamed, it would be the person who sent it in late, not the student who requested it.