If you have the same order of cables on both ends, it's a straight through cable. If you use A on one side and B on the other, it's a crossed cable (although the order is hardly random, obviously, but I suppose you knew that). The point is, the cables inside your UTP cable are nothing but copper, it doesn't matter what color the isolation is. The electrical signals passing through don't care about colors.
It will work just fine, but there is a standard in place to easily recognize what kind of cable you're dealing with and to make sure you don't mess up when making crossed cables. I'm sure there's more complicated reasons as well though, but the RFC or what not should help you out if you want to know more. :-)
EDIT: Massimo replied that it might in fact make a difference after all: the 4 pairs of cables are, according to him (I did not know this before and didn't doublecheck) twisted differently. This twisting makes sure the electromagnetical interference is reduced to a minimum (also the reason you want to make the untwisted part when making the cable as short as possible).