They will definitely first and foremost look at your undergrad gpa. If it passes muster, they will look pretty keenly at how you did in your undergrad science pre-reqs. The MCAT is probably equal or slightly lesser weight. Then perhaps ECs, LORs and essays. That's assuming that your grad degree gpa is ok, just not stellar. If it's stellar, and especially in the sciences, then great - it'll definitely be a plus.
Now, if your grad degree gpa is not so hot, and was in the sciences, it may have a bit more impact than if it's in something completely unrelated (law, business, etc.). If you failed out or left the grad program, you're probably going to have to do some explaining (especially if it's in science).
From my own personal experience, it never came into play. My grad gpa (law school) was not so hot due to having a little too much fun my third year after I secured a job already. I think I ended up graduating with a 3.2, but no one every brought it up or questioned why I got mostly As my first two years, and Bs and Cs my last year.