How to Choose a PhD Program
By Ya'el Courtney, PhD | Stanford Postdoc, Harvard PhD in Neuroscience
Last updated: March 2026
If you're reading this, you probably have multiple PhD program offers in hand, and April 15 is getting closer. Congratulations — that's a wonderful problem to have.
But it can also feel paralyzing. You're choosing where you'll live, who you'll work with, and what your daily life will look like for the next five to seven years. Every program you visited seemed great in its own way. Everyone you talked to said "you can't go wrong." And yet here you are, trying to make possibly the biggest decision of your early career with incomplete information.
I've been there. I applied to seven biomedical PhD programs, was admitted to all seven, and ultimately had to choose between Harvard and Stanford. I now coach students through this exact decision every year. Here's the framework I use — both from my own experience and from watching what actually predicts whether someone thrives in their program.
Start With What You Can't Change
Some things about a PhD program are structural. They won't bend for you, no matter how much you like everything else. Start here, because these are the factors most likely to create real friction over five-plus years.
Funding. Is your funding guaranteed for the full duration of the PhD? Some programs guarantee five or six years; others guarantee two or three and expect you to secure external funding or be supported by your advisor's grants after that. This matters more than people think. Being in a lab where your advisor is stressed about whether they can pay you creates a very different dynamic than being in a program where your stipend is locked in regardless.
Stipend vs. cost of living. A $40,000 stipend in Houston and a $52,000 stipend in Boston are not the same thing — and depending on rent, the Houston student might actually come out ahead. Look up actual rent prices near campus. Can you afford to live alone, or will you need roommates? Will you need a car, and can you afford one? I loved my time at Harvard, but I'll be honest — on a $43,000 stipend, I could not afford to live alone in Boston. Roommates weren't a lifestyle choice; they were a financial necessity. Stipends have gone up since then, but so has rent. That's the kind of thing you should know going in rather than figure out after you've committed.
Program structure and requirements. How many courses are required, and when? Is there a qualifying exam, and what does it look like? How are rotations structured — how many, and how long? Some programs front-load coursework heavily in the first year, which can feel overwhelming if you're also doing rotations and trying to figure out your thesis lab. Others spread it out. Neither is objectively better, but one might suit you better than the other.
Rotation systems. If you're in a rotation-based program (most biomedical PhD programs are), pay attention to how rotations actually work. How many rotations do you do? Are they one-on-one with a PI, or more flexible? What happens if your top-choice lab is full after rotations? Some programs have strong norms about PIs taking rotation students; others are more competitive. This is a great thing to ask current students about honestly.
Unionization. Whether graduate students at an institution are unionized — and if so, what their contract includes — can meaningfully affect your quality of life. Graduate student unions have driven some of the biggest recent improvements in PhD compensation and benefits. Harvard's stipend jump to $50,000 came after sustained pressure from HGSU-UAW. Cornell's contract locked in dental, vision, and transit benefits. Northwestern's union won expanded childcare grants for student parents. Beyond pay, union contracts often establish formal grievance procedures, workload protections, and clearer expectations around things like TA hours — structures that can matter a lot if you ever find yourself in a difficult situation with an advisor or department. This isn't a reason to choose or reject a program on its own, but it's worth knowing whether a union exists, what the contract covers, and how active it is. You can usually find this on the graduate school website or by asking current students directly.
Then Assess What Shapes Your Daily Life
The structural stuff sets the boundaries. But within those boundaries, your day-to-day experience is shaped by people and culture — and these are harder to evaluate from the outside.
The student body. Did you like the other students you met during your interview or recruitment weekend? Could you see yourself grabbing coffee with them, venting to them after a bad experiment, celebrating with them after a good one? I cannot overstate how much this matters. When the pandemic hit four months into my PhD, the fact that I genuinely liked my cohort — and had moved in with three of them — made an enormous difference. Your cohort will be your primary support system in ways you can't fully predict.
Student happiness and culture. This is the single most important thing to assess, and also the hardest. During recruitment weekends, programs put their best foot forward. So how do you get honest answers? A few approaches that work:
Ask older students — third-years and beyond — directly: Would you choose this PhD program again? What’s something you wish was different about the program? Pay attention not just to what they say but how they say it. Do they hesitate? Do they give a real answer or a rehearsed one? Ask multiple students the same question and see if you get consistent answers.
Ask about students who left. Every program has some attrition, and that's normal. But if multiple students left the same lab, or if people get uncomfortable when you ask about it, that's information.
Ask about mental health resources and whether students actually use them. A program can have a counseling center, but if the culture discourages people from accessing it — or if wait times are months long — that matters.
Faculty you'd want to work with. I always tell prospective students: make sure there are at least three PIs you'd be genuinely excited to work with. Not just one dream lab. Things change — PIs move institutions, labs fill up, a rotation doesn't go the way you expected, your interests shift. Having multiple strong options gives you flexibility and reduces the pressure on any single rotation to be "the one."
If you're already pretty sure you want to work with one specific person, that's fine, but be honest with yourself about what happens if it doesn't work out. Is there a backup plan at this institution that you'd still be happy with?
Advisor-student dynamics. If you've already identified PIs you're interested in, try to learn about their mentoring style. Do they meet with students weekly or are they more hands-off? Do their students publish frequently, or do they tend toward fewer, larger papers? How long do students typically take to graduate from that lab? Where do former students end up? All of this is publicly available information — lab websites, LinkedIn, asking current lab members — and it tells you a lot about what your experience would actually look like.
Consider Your Whole Life, Not Just Your Science
You're not just choosing a program. You're choosing a city and a lifestyle for a significant stretch of your twenties or thirties. That matters.
Geography and proximity to people you love. How far will you be from family, a partner, or close friends? How do you feel about that distance? Some people thrive with a fresh start in a new city. Others underestimate how much they'll miss their support network when things get hard — and things will get hard at some point in a PhD. There's no right answer, but be honest with yourself rather than dismissing it as a secondary concern.
The city itself. Can you picture yourself living there beyond the walls of your lab? Is there outdoor space you'd actually use? A food scene you'd enjoy? Communities you'd want to be part of? I chose Boston knowing the winters would be rough and the cost of living would be high. Those things were real downsides. But I also loved being in a city with an absurd concentration of research institutions, easy access to hiking in New England, and a bus ride to New York. The tradeoffs were ones I could live with.
Partner and family considerations. If you have a partner, will they be able to find work or continue their education in that city? If you're planning to start a family during your PhD (many people do), what are the parental leave policies? Is housing near campus family-friendly and affordable? These aren't secondary questions — they directly affect whether you can sustain a PhD long-term.
What Not to Optimize For
Rankings. US News program rankings are, at best, a loose proxy for program quality and, at worst, completely misleading for your specific situation. A program ranked #3 nationally might be mediocre in your subfield, while a program ranked #20 might have the three best labs in the world for your research interests. Rankings also don't capture mentorship quality, student culture, or any of the things that actually determine whether you'll be productive and happy.
Prestige for its own sake. I went to Harvard and I'm glad I did — but I went because of the specific program, the specific people, and the specific fit, not because of the name. If I'd chosen Harvard over a program that was clearly a better match just because it was Harvard, that would have been a mistake. The name on your PhD matters far less than the quality of your training, the papers you publish, and the network you build.
One dream PI. I've watched students choose a program almost entirely because of one lab — and then have that rotation not work out, or have the PI leave the institution, or realize the mentoring style wasn't what they needed. If you're choosing a program primarily for one person, make sure you have a genuine backup plan that you'd still be excited about.
A Framework for Actually Deciding
When I was choosing between Harvard and Stanford, I was stuck for weeks. Both were incredible programs. Here's what ultimately helped me — and what I now walk my coaching clients through:
Write down your non-negotiables. Not your preferences — your hard requirements. For me, these were: guaranteed funding, at least three labs I'd be excited to join, a rotation-based program, and a city I could afford to live in (barely, in Boston's case). If any program fails a non-negotiable, it's out, regardless of how shiny everything else looks.
Talk to people who know you well. I'm an external processor, and talking through my decision with friends, labmates, and mentors helped enormously. Not because they told me what to do — but because explaining my reasoning out loud helped me hear what I actually cared about. If you keep coming back to the same thing when you talk about a program ("but the students were just so happy" or "I keep thinking about that one lab"), listen to that.
Pay attention to your gut after the visits. Which campus did you feel most at home on? Where did conversations flow most naturally? Where did you feel most like yourself? These impressions aren't irrational — they're your brain integrating a lot of information that's hard to articulate on a spreadsheet.
Remember: there is probably no wrong choice. If you're deciding between multiple strong programs, you will very likely thrive at any of them. The best scientists are happy scientists, and happiness comes from choosing a place that fits your values and your life — not from picking the "objectively best" option, which doesn't exist. The decision feels enormous right now. Five years from now, you'll barely remember the stress of making it.
After You Decide
Once you've made your choice, do two things promptly:
Accept your offer and let the program know you're coming. They'll be thrilled to hear from you.
Decline your other offers as soon as possible. This is genuinely important and genuinely kind. Programs have waitlists, and every day you hold an offer you're not going to accept is a day someone else is waiting anxiously to hear whether they got in. I declined my other offers within a few days of making my decision, and I'd encourage you to do the same. A brief, gracious email to the program director is all it takes.
Then take a breath. You just made a big decision, and you made it thoughtfully. Whatever comes next, you're walking into it with your eyes open — and that's the best position to be in.
Choosing a PhD program and want help thinking it through? I offer one-on-one coaching sessions for exactly this kind of decision. Sometimes an hour with someone who's seen dozens of students make this choice is all you need to get unstuck.
