Does doing poorly in a course hurt my chances of getting into grad school?

I am a tenured associate professor in the mathematics (note: not chemistry) at UGA and did graduate admissions for several years there.

I am a little surprised that the two answers so far have avoided the obvious: getting a C- grade in two required courses in your major certainly has a negative effect on your chances of getting into graduate school. The only question is how much. I don't want to speculate on this because you deserve answers from my opposite number in a chemistry department, and I hope you'll get one. I'll just say: if we "transposed" this question into mathematics, getting C- grades in two core courses that are well known to be difficult enough to knock some students out of the major (say, real analysis): that would indeed be a serious flaw. We can admit students who got good grades in all the key courses, and we usually do.

However, I don't think you have asked exactly the right question. The issue is not whether you should abandon your graduate school plans based upon your performance in one (or two) courses. You shouldn't. But trying to precisely quantify the damage is our job, not yours. Your job is to avoid if possible, and if not possible remedy, the problem.

For a very serious student (students who want to go to grad school should count as "very serious"!), getting a C- in a course and then moving on to take the continuation course with the expectation of more of the same is a tactical error. You say you plan to retake the courses anyway. Then why are you even taking the second course now?!? You need to plan more precisely for your own success. I would look into withdrawing from the second semester course if it's at all possible.

You also mention health problems. They can certainly affect your academic and professional performance, and this can happen in an uneven way. It is quite plausible that you're doing as well in the other courses that you have more talent / experience with / predilection for as you would have done if you were healthy and doing much worse in the course that needs more of your time and energy. Really consider taking time off, or adding a semester or a year, or doing whatever you can to lighten your load and give yourself the chance to do well. It is much easier to get official accommodations for serious problems while they're occurring than to try to explain two years later the dip in your transcript.

In general I think you could get better advice on which courses to take when and how to succeed in your major. A lot of the most successful students are successful not because of superior talent but because they've been properly mentored or set up for success by others, or because they instinctively know much better than others how to set themselves up for success (which, contrary to what I said above, is certainly a talent).

Good luck.

The short answer first. It hurts, (particularly a D or F) but does not necessarily rule out chances at a PhD program in chemistry.

I'm a tenured associate professor in chemistry at University of Pittsburgh. While I have not served on the admissions committee in our department, I have been chair of graduate recruiting. (Our department separates these two.) Full disclosure that independent of Stack Exchange, Melanie expressed interest in our department.

Most graduate programs have a minimum GPA required for admission. Our university requires a 3.0 GPA or higher from undergraduates. We absolutely cannot consider students with a lower GPA, regardless of qualifications. My advice to such students is to find a master's program or take further courses to provide an improved GPA. Students are admitted to our program with mediocre undergraduate performance, followed by high-quality master's work.

I won't lie. Assuming your overall GPA and grades in the major are good, receiving a C and an F in your major would still raise some concerns. That said, a personal statement is an excellent opportunity to explain extenuating circumstances (e.g., illness, family obligations.. various life events). Recommendation letters can also help in this regard.

My final conclusion is that it would depend on the quality of the rest of the application. If, for example, you achieved well in other courses, say several A's, quality GRE scores, and/or had an undergraduate publication or two, it's easy to overlook a stumble.