Are you going to the same school? If so, it shouldn't be much of an issue. But if you're not, it's likely a deal-breaker, unless you're in the same area. You might work it out, but it's not likely. College relationships actually fare better, because there is the opportunity for one person to transfer. In grad school, that's practically unheard of.
If you can work out the logistics, it's not a problem. I chose to delay applying a year because my fiance will finish grad school in May 2011. This gives us time to get married, and he can come with me to med school wherever I'm accepted. It allows me the luxury to apply broadly.
I know a couple in my major who I'm really rooting for. I rarely view relationships between 22-year-olds this way, but they're perfect together. He's applying to med school and she's applying to pharmacy. If they can't make it work, I'll be really sad for them. But that is reality. You shouldn't sacrifice your dreams for someone unless your dream is to be with them, and figure the rest out later. That has to be a carefully planned decision, because it's not worth sacrificing your own goals and happiness...you'll only resent your significant other, even if it's not her fault...