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My area of research can fit pretty well with both CIHR and SSHRC, depending on how I tailor it. I'm applying to grad school this year and initially planned to apply for CIHR CGS-M, but would it be better to apply for SSHRC if my research meets their criteria? I've always heard that CIHR is harder to get, and most schools do have way more SSHRC scholarships. 

Basically, I'm just wondering if CIHR is significantly harder to get than SSHRC at the masters level. 

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Are you a current Masters student applying for their 2nd year or an undergrad student applying for the first year?

If you are a current student, then your advisor should know best. Apply to whatever agency has been funding their own research program. 

If you are an undergrad (or not yet a graduate student) then you can ask potential advisors and try to find out what students in your future department tend to be funded by. Sure, there are way more SSHRC awards, but there are also way more SSHRC applicants.

I'm writing this from the NSERC vs CIHR point of view as many of my friends have overlapping interests. They have told me that fit with the agency is really important. So it doesn't really matter whether there is more of one award or another, if the evaluation committee doesn't feel that your research is a good fit with the agency, then they won't fund you. So I'd say find out which agency tend to have funded your research topic in the past and what people in your department have received in the past and go with that.

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Hi, 100% agree with TakeruK! CIHR tends to be "harder", because most Canadian universities receive less allocations for CIHR compared to SSHRC. Assuming you are asking in the context of a undergrad aiming for Master's funding in your application, take a look at the schools you want to apply to, and the potential supervisors. If they tend to be funded more by a certain agency, it makes sense to leverage your proposal to that. On the other hand, if you generally have interest in one over the other, then capitalize on that and write your proposal such that the research is more social or more health-oriented. I had that same dilemma between CIHR and NSERC just last year (when I applied for my first year Master's). I ended up choosing CIHR, because I wanted to gear my proposal to a clinical and health-related research project. Turns out it was a great idea :) 

Remember, you can only choose one! So look at all your schools, see which one makes the most sense and you can cover the most bases, and write it for that agency!

Good luck!

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Another thing you might want to check is quota. Some departments might only have a quota for a specific council. I was deciding between CIHR and SSHRC, too, but that decision was taken out of my hands when I found out the department I was interested in didn't have a SSHRC quota so I automatically defaulted to CIHR. Then it became a question of tailoring my question to meet CIHR's eligibility.

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