I have (as the title suggests) a gigabyte ga-ep45-ud3L Motherboard. The BIOS/CMOS is seated right under my eVGA geForce 8800 GTS video card (which seems to be a very bad design flaw IMO) causing it to reach temps of 60C+. I know this is hot, but I cant help but think the designers HAD to know this would happen. There is only one PCIE16x slot on this mobo and I dont have a choice as to where the graphics card gets to go. The back of this graphics card is very hot to the touch.

So, with this in mind, I was thinking of getting a 4pin system fan and just rigging it up to sit there and blow air on that spot. Im assuming that would be fine, but I wanted some observations from some more tech-savvy people. More importantly, has anyone else encountered this problem with these mobos?

I use the same motherboard with a 9600 video card, with no heat issues. It may be the video card itself that is causing this overheating. My case has a 120mm front and rear fan. The Nvidia 9600 has its own fan, and it runs cool

My card also has its own fan, but it runs VERY hot. I cant touch the back side of it for more than a second or two. Apparently this is par for the course with these GPUs. I added a spot fan with has dropped the BIOS/CMOS temp 10C or so, but even with no computing or anything happening it runs at 45C (55C when gaming).

Did you just build this system recently? I upgraded my system with this motherboard last month. Your 8800 might have its fan/heatsink improperly installed or assembled with no thermal compound

Add more case fans.