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If I were you I would hold off on doing a masters until residency. Most (if not all) of the programs you mentioned would allow for you to take time out of your residency to do this. You would also get funding for it! Win win.

 

If you do decide to take this gap year during undergrad medicine (if your program will even allow it... I've never heard of anybody doing this, but that doesn't mean anything) then I really don't think it would hurt you. If anything it will be something that sets you apart.

 

As far as getting face time in Canada, I feel like this gap year is totally independent from your ability to do that. I'm assuming you will complete your clerkship back in Canada and thus can use your elective time to visit Canadian programs just like everybody else does. You won't be losing any time in Canada by doing this... so I'm not sure why you think you'd be disadvantaged that way.

 

Finally, I don't think doing research in the States will be seen as "weird" (i.e. rather than doing it in Canada). I really don't think they care where you do it, as long as it's at a credible institution.

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What you could look into is Clinician Scientist streams in residency - I think that is how people generally do that here, that or MD/PhD, rather than taking a year off in the middle on your own.

 

You can often pursue a masters even in programs that don't have the official "clinician investigator" designation. So you don't need to limit yourself to those programs if you're really set on doing heavy research.

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