3.8 GPA, but 3 Fs and 1 D on transcript So here's a funny thing: I have 3 Fs and 1 D on my transcript, but my GPA is ~3.8, which is "high" because I double majored in math and computer science. The reason for those 4 bad grades is that I had 2 bad semesters where I suffered from depression; I didn't drop the classes before the deadline so I ended up failing the classes. However I retook the classes and got As in them (hence my GPA), and in fact got A/A-s in all subsequent classes (quite an improvement). I plan to apply to a master's for computer science, and eventually a phd. However I know the admission officers eyes will bleed when they see my transcript, despite my GPA, because my school keeps ALL grades on transcripts, even if the grades were replaced by retaking classes. Do I still have a chance at top-10 graduate school for computer science even with these grades (which were retaken and then aced)?
In my (rather extensive) experience with graduate admissions, admissions committees understand that people have semesters in which life interferes with school. If you've retaken the classes and received high marks in them, this very clearly signals that something was interfering with your performance during those two semesters and that the bad grades have nothing to do with your underlying ability. Those grades won't go unnoticed -- but nor will they hurt you the way they would had you not repeated and aced those courses. 

It would help further if you have a trusted mentor who could mention and--to the degree that you comfortable, explain--this issue in his or her letter of recommendation. 

Don't count on cruising through the application process, but also don't lower your ambitions based on these grades.