AFAIK yes. Once you plug it in, the computer will recognize both partitions and ideally automatically assign drive letters to each.
Do you have to see both partitions on whatever computer you're using? If not, may I suggest you format one partition as HFS+ and the other as NTFS? FAT32, though compatible with both OSes, has a 4GB file-size limit.
Actually I was mistaken in my first post. Mac OS X can't read NTFS partitions. But like you said, they're separate. So it's no biggie.
Again OP, if you want either computer to see everything you place on the hard disk, you'll have to use FAT32, as its the only format understood by both Windows and OS X. Then again, watch out for that 4GB size limit!