The MBR area can be altered by malware so that Windows systems cannot boot properly. It is important to keep this area protected and clean as noted below:
Master Boot Record – Importance of protecting against malware
QUOTE: It is that time of the year again to start anew. In terms of personal computers, the act of restarting the machine is called a reboot – an action that triggers execution of code from a special part of the disk called the Master Boot Record (a.k.a. MBR). As the year 2010 ended, I looked at some of the threats targeting the MBR. The MBR, the most important data structure on the disk, is created when the disk is partitioned. The MBR contains a small amount of executable code called the master boot code, the disk signature, and the partition table for the disk.
The master boot code performs the following activities:
1. Scans the partition table for the active partition.
2. Finds the starting sector of the active partition.
3. Loads a copy of the boot sector from the active partition into memory.
4. Transfers control to the executable code in the boot sector.”
HOW TO FIX A DAMAGED MBR