The best way is to first install the Windows, because the bootloader needs to be in the mbr on the first harddrive. Then you can go ahead and install any other Linux distribution on another partition. To boot the two different systems use either Grub or Lilo bootloader provided by Linux. Assuming Windows XP/Vista is on the first harddrive and first partition of your sata drive: Entry for Grub: title Windows XP rootnoverify (hd0,0) makeactive chainloader +1 Entry for Lilo: other = /dev/sda1 label = Windows XP table = /dev/sda To remove Grub or Lilo from the mbr you can run in Windows: fdisk /mbr