We can analyze any answer to your question in the following way:
a computer is simply some hardware that does nothing unless instructed to do.
BIOS tells the computer to do something. So, BIOS can have malicious code. You bought a new computer, you don't expect it to be contaminated. You can protect it in modern computers, so that it isn't upgraded if you don't do some specific manual commands. Just upgrade bios from the manufacturer site after being very sure they haven't being hacked, and BIOS won't cause you problems. (In the past there were BIOS virus, like chernobyl).
Operating system tells your computer to do something. Again, you expect it to come clean from manufacturer. Don't update it except after being sure the manufacturer is clean, and you're good.
OS have some holes on it and on it's drivers. They have many programs running (like network drivers, sharings, etc) that can receive malicious commands from a network. Don't connect it to any network (wired or wirelles, including bluetooth) and you're ok.
These same holes can occur from drivers or programs that are runned from USB. Be sure to what you'll attach to your USB port and you won't have problems. (There's being reports of a malware that come inside a digital photo frame, so yes, you'll never know where the problem can come from).
Firewire ports can have direct access to your computer's memory, since it can access DMA. Take care with them.
The same applies to PCMCIA cards.
You'll install programs on your computer. Really check them with antivirus.
Documents can carry virus inside them, specially because programs that open them (office, pdf readers, etc) can have vulnerabilities. Double check them.
And them, this will warranty you protection?
No, you won't be 100% protected.
Because antivirus check for know virus. One virus specially designed to get you, probably will.
USB - Firewire - PCMCIA - any other port: can too be attacked somehow, with specially designed chips carrying special codes.
Softwares like the operating system and all the other programs can have vulnerabilities that are not know neither protected. Read about zero-day vulnerabilities and you'll know about it.
And, finally, read something about the Stuxnet virus. Let's say, Iran probably did take care with it's nuclear facilities, and even so got infected with the best (worst?) virus crated so far, probably by enemies intelligence army.