A polyrhythm is basically a complex rhythm made up of at least two or more completely different rhythms playing off of each other, simultaneously. They are usually (if not always) different time signatures.

African and Middle Eastern music tend to use a lot of polyrhythms in their music, as they hardly adhere to the same "standard" metrics as Western music does. This is what everyone was talking about above where you have to worry about which bars the patterns actually loop and land on.

There are a couple rules for how to subdivide the rhythms so that they work together properly..
A quick google search found me this, which will help explain it much better:
http://www.xs4all.nl/~marcz/Polyrhythm.html
And another good one:
http://fusionanomaly.net/polyrhythms.html