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second this. DownstateIn terms of research opportunities they seem on par; Downstate's location makes it easier to find research but Upstate's administration seems more supportive and willing to help students. I'd say in terms of overall clout (if you're trying to match in NYC), Downstate wins this hands down.
Another thing to consider for Downstate is their 1.5 year preclinical curriculum and their stellar clinical education, which will undoubtedly help with P/F Step 1 and Step 2 (since PDs will most likely use Step 2 scores to gauge applicants now.)