Post Bachelor vs. Upper-Level Science Classes

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Since you're posting in the DO form, I'll say to retake the pre-req courses you did poorly in. After getting A/B's in those prereqs your sGPA will probably be good enough to start applying to DO schools. You could do the upper level courses if you still feel like your cGPA isn't where it needs to be. But, if you take the upper level courses and do poorly in them, it might do more harm than good.

I see post-baccs/SMPs as the final alternative to get into MD schools because MD programs don't accept grade replacement. There are some post-bacs, however, with linked programs to MD/DO schools (like being guaranteed an interview). But if you're mostly applying to DO schools, save your money and simply retake the prereqs at a community college.
 
I have similar stats as you, kind of. I have cGPA 3.45 and sGPA 3.07, and I also plan to take the MCAT in spring '16. What I am doing is retaking science classes that I got C, which are 3 classes, and plan on taking biochem and genetics as well as upper div science classes. I chose the DIY postbacc route because it is cheaper and it actually raises both your GPAs tremendously. Also, I have read and heard from different people that doing a formal postbacc program and not doing well in it will shoot your chances of getting an acceptance anywhere, because it shows adcoms that you can't handle med school classes. So if you have the money and you can guarantee you'll do great in the postbacc program then go for it, otherwise don't.
 
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