While most XP installations only use one hard disk and one partition, Windows refers to two different kinds internally: a system partition, and a boot partition. Those terms are confusing and non-intuitive. Basically the system partition boots the computer and the boot partition holds the system.

details of the boot partition

The boot partition is a very complex organization of directories and programs that I cover in another tip (node/92).

The system partition must always be on the first hard drive in the system and must be an active primary partition. The boot partition can be a primary partition or a logical drive within an extended partition.

In most cases, those two partitions point to the same physical partition.

details of the system partition

The system partition does not include any folders. It exists as a root folder only with three or more files. Having additional folders in the system partition does not affect the operation of boot files.

You might notice that the files in the system partition are among the files found on an Emergency Repair Disk (ERD). This should not be surprising because an ERD is used to restore files to the system partition if these files are corrupted, deleted, or otherwise destroyed.

source: The Windows XP Layout; 2003 by Stu Sjouwerman (Que)