How many gap years? Unique situation

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Three years will look better. Personally you sound like you're in the 21-22 age range so you're not going to be too behind. The real question you have to ask yourself is why MD/PhD instead of an MD (with research)+research intensive residency/fellowship. Your MCAT will be a significant deciding factor, so I can't comment too much beyond that.

I personally was 4 yrs out of UG by the time I started med school and I had 3 yrs of UG research + 2 yrs industrial R&D experience + 2 yrs of a masters. I can't say I regret the gap years. It helped me mature and I know I sure as hell wasn't ready for med school straight out of UG.
 
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