Windows 2000 and XP are very picky about the hardware they run on and, in most cases, rebooting these operating systems after swapping out your motherboard will result in a boot failure and BSOD (blue screen of death). There is however a way to avoid re-installing Windows and that is doing a repair installation. After swapping out your motherboard and sucessfully getting to the BIOS, ensure that the boot order includes the CD-ROM. Then, insert your Windows installation CD into the drive and reboot. For XP users, do the following once booted to Windows Setup:

(1) Press ENTER to setup Windows XP now.
(2) Press F8 to agree to the EULA.
(3) Press “R” to begin a repair installation.

At this point, it will go through the entire setup process as usual, but what it is doing is simply re-installing all of the system files. All of your user settings, registry and data will remain intact.

Once the installation is complete, XP users will need to re-activate their installation of Windows with Microsoft once again. Once this is done, you will also need to run Windows Update again to re-patch Windows. After this, you should be up and running.