Can I get away with a few blemishes on my record?

[c12]

I'm currently about to start my junior year (undergrad). I know for sure that I want to go to grad school, and I'm trying to get a head start on the process as much as I can. The big concern I have at the moment: I have a few small questionable spots on my transcript.

The past year or so has been really hectic for me. I've been really sick and have spent most of the past year in and out of doctors offices non-stop. We've gotten to the point where things are finally looking up...some of my problems have been resolved, and we've finally found the right mix of medications to take care of the others. But during the span of time when I was ill, my academics suffered slightly, so I can't claim a great sophomore year. My load got a bit too heavy during the year, so I ended up switching to audit mode for a couple of my classes (one each semester). These classes weren't ones that I could pass off as having taken for my own fulfillment or anything like that, so I'm sure it will essentially look the same as having two Ws (and to be fair, I guess that's what they technically were). I also got a D in one of my gen ed math courses during summer term. It's just a gen ed, not a class important to my major, and I don't think it's even a requirement for any of the grad programs I've looked at. But still, I know a D is never good.

My overall record is good. I have a 3.45ish, and only a few Cs (mostly all As and Bs). I do well in my major, which is what I'll be primarily taking classes in for the next two years, so I think I could even bring it up a few points more (I could envision maybe a 3.6 or so by the time I apply). I tend to do well on standardized tests, so I have high hopes for the GRE as well.

I don't know how to treat this, so I have a few questions:

1. I'm not looking to get into top schools. I'm not after prestige. I just desperately want to be able to continue my education. So at the average school, would a few blemishes on my record be enough to mess with my admissions chances, if my record is good otherwise? So many people have told me that I'll be fine since I have a good overall GPA, but I can't help but be skeptical...as having a D, 2 audits, and a few Cs (actually, one of them may have even been a C-) isn't exactly regarded as a good thing.

2. Should I try to have my circumstances explained? I know that undergraduate applications usually have a space for you to explain any special circumstances, but I haven't really seen this on grad schools apps so far. I'm sure there's some way to have my medical issues accounting for (mentioned in recommendations, perhaps?), but I'm not sure if I should. Part of me thinks that my GPA is high enough that I shouldn't bother, because it might seem like I'm trying too hard to make excuses for what is technically only one bad grade. But another part of me feels like I should absolutely account for the blemishes, no matter how minimal they are, so that schools know that I can do much better. Thoughts?

Any advice would be greatly appreciated.

[aginath]

The clock really starts ticking from this year forward. Most schools are concerned about your last 60 hours (that's when you start to hit your specialization instead of general/core curriculum); that translates to your junior/senior year for most people. Don't worry about the past right now. Just keep on keepin' on. Work work hard from here on out and you should be alright.

[TheDude]

Don't freak C12. Use me as a case study so far:

I have a couple C's and a D on my transcript from 2.5-3 years ago. I'm not worried at all. I ended up graduating Cum Laude with a 3.59 Overall GPA (3.8 the last 2 years) and a 3.8 in my degree focus classes. I won't lie, I think the grades held me back from higher distinctions overall when I graduated. Insert A's in those classes and I am graduating Summa Cum Laude (missed it by .01).

However, I did a lot of research and made things happen on other levels academically. My GPA isn't going to keep me out of Ph.D programs- maybe for the highest tier, but you can still do other things to show that you are perhaps a more viable candidate than someone who has a 3.8 and didn't do those things.

If you are 2 years out don't freak you are perfectly fine.

If you are applying to Ph.D programs 2 years out don't get your hopes up in terms of a couple schools because potential advisors might not even have space for new people. I thought I had my list of schools and after initial salutation letters to faculty it changed quite a bit.

Keep doing what you do!!!!