As with any decision this sizeable, with MD PhD programs, there is no one right way of going about choosing which institution to attend, but here are some things to think about:
1) Location: Most MD PhD programs take 7-10 years to complete. That’s a significant chunk of your life, nearly 10%. So while you have to balance a lot of things when making your decision, think whether you want to live somewhere during a period of your life where you might enter single but leave married. When you interview, we encourage you to consider spending an extra day walking around town at programs you are seriously considering.
2) Clinical Program: Most MD PhD applicants come to the application process with a very research-oriented mindset. They look up labs, PubMed professors, and so on. That is all certainly important, but don’t neglect evaluating the clinical program as well. The reality is that you will be spending nearly 50% of your time as an MD student. Consider the following: Is the school pass-fail? Is the curriculum a block schedule? How much problem-based learning is involved? Are the medical students satisfied with their experience? It’s important to make sure that you will be happy with your clinical training.
3) Research Years Support: This can vary widely between institutions and can truly affect your experience, so ask about these details. How are you funded during your PhD years? PIs love students who are essentially “free” to them and are supported through a medical scientist training program (MSTP) rather than their own grants. Thus guaranteed PhD support means you will be welcomed much more heartily by potential research mentors.
Ask whether you will need to teach during your PhD years. Teaching responsibilities can take you out of lab and thus slow down your research. How many graduate classes do you have to take to full-fill your PhD requirements? Finally, ask whether the MD-PhD program expect its students to have a full-on PhD experience with lots of floundering at the beginning which may take 5+ years to achieve, or do they have a general understanding that you have an exceptionally long road ahead of you and are they ok with shorter, faster PhDs that take 3-4 years.
4) Flexibility with the transitions: This may seem like a minor detail but one that can add a whole year to your training. In some programs, your re-entry back to the third year of medical school can only happen in July, even if your PhD is on track to wrap up in October. This can either make you really rush to try to rapidly defend and publish your paper or will force you to lounge around in lab for months unnecessarily. Some in this situation will have the urge to force a faster exit from lab in July, but this can leave papers unfinished and once you leave the lab, even with the best of intentions of your co-authors, projects may never get done or simply die in review, leaving you without a publication you would have otherwise had. Alternatively, some schools will let you come back to the third year of clinical rotations mid-year, and given that the last two years of clinical work in most schools really amounts to 1.5 years of true clinical contact-time, this can allow you to save a whole year.
In summary, there is no right way to make such an important decision in your life. You will enter an MD PhD program in your early twenties and you will graduate a completely different person, physically, mentally, and emotionally. While your classmates’ lives rapidly evolve through medical school and residency, yours will seemingly remain static. So try your best to think about what is truly important to you, and make your best effort to match your decision to those core life values.