As I start my second year of the program, I figure it is time to write this very belated post on how I chose where to apply. Before you apply for MD/PhD programs, make sure that you are certain that is what you want. You can read why I chose the MD/PhD route here. Also, I want to preface this post by saying that I love organizing and lists. If you are not as much of a fan of these things as I am, then maybe my decision-making methods might not be as helpful for you.
Step 1: Find All the MD/PhD Programs
Before starting I wanted to see all my options, I used a list like this one and other AAMC sites to go through all MD/PhD programs.

Step 2: Make a list of schools with programs you want
I knew that I wanted to do my PhD somewhere in the realm of neuroscience. This meant that I put every school that offered a PhD in something neuroscience-esque was put on my initial list.
Step 3: Remove schools that do not have research that interests you
I am interested in a lot of things so this was not going to narrow things down too much; however, I also knew I wanted to do human subjects research (no animals or other bench work), so I was able to cut at least 20 schools from the list using these criteria.
Step 4: Look at the med school environment curriculum
Do you prefer a systems- or subjects-based approach? Do you like traditional classes or PBL? Would you prefer a larger or smaller med school class? What about volunteering and clinical experiences? I used my preferences (traditional, subject-based classes with non-required lectures, larger class size, and plenty of opportunity for volunteering and clinical work) to further narrow down my list.
Step 5: Research the schools admission stats
At this point I had a spreadsheet with about 40 schools and I created a spreadsheet with the location, name of specific PhD program, average accept MCAT and GPA, how many applicants apply, are interviewed, and accepted. This type of information and any other details that are important to you. Also make sure to note whether it is MSTP or not and how funding works (not all MD/PhD programs are fully funded).

Step 6: Color-coding
I divided the remaining schools into 4 color groups based on how my stats compared to their average stats. Green was for schools where my stats were above theirs, orange for when my stats where about the same, and I think you can get an idea of what pale red and red meant.
Step 7: Establish your preferences
Everything is color-coded and organized, but there were still over 40 schools, so how to narrow it down? At this point, I bolded certain things that were important to me (for instance, particular locations or program that really stood out). There were some neuroscience programs that were 100% human-focused and some that incorporated ethics. I also knew that I really wanted to live in a city and would much prefer to rely on walking or public transit than a car.
Step 8: Narrowing down the list
This is where you set your own limits based on your finances and time. I decided a set number of schools to which I would apply and then allowed myself a certain number of schools from each color category (the most came from green, and the fewest from red).
Step 9: Apply!
This is where my obsessive spreadsheets were especially handy. I kept notes of all deadlines and when exactly I submitted my secondary applications and when I would expect to hear back from each school. This helped reduce paranoid school portal checks.
Also, I kept a spreadsheet with every question/essay prompt I had to write about and how many words and characters each was. It’s amazing how similar many of the schools’ questions were.

Well, that was my method. I find it helpful to organize and make lists, so if you do, too, then this may work for you. I found the MSAR to be invaluable for putting together all this information. There are also a few online forums that can also be helpful wherein people talk about their experiences at different schools and with the application process .
If you have any questions about how I chose where to apply or why I applied in the first place, feel free to contact me!