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My undergraduate GPA is 2.93 from Fall of 1999. (I am an older student.) I will be getting my Masters in Physics this fall and my GPA is about 3.5. I'm planning to apply to PhD programs for Fall 2013. Since I will have completed a higher-level degree, does the undergraduate GPA minimum of 3.0 still automatically disqualify me or will they allow me into the applicant pool based on my graduate GPA?
No one is really automatically disqualified. Recognize that your undergrad GPA still matters (and a 3.5 isn't amazing for a masters program), but apply to wherever you feel is a good fit for your application otherwise.
I'm pretty sure I have heard that if the entire graduate school enforces a minimum GPA requirement, the individual department needs to get permission (from the dean maybe?) in order to admit someone under that GPA. In other words, the rest of your application needs to be good enough so that the department is willing to put in extra work for you.