A rootkit is a software program or coordinated set of programs designed to gain control over a computer system or network of computing systems. In virtually all cases, the purpose and motive being to perform any manner of malign act upon a host computing system. The term rootkit is actually a compound word derived from - and originally referring to - the administrative (superuser) account (or "root" account) in historical operating system terminology - primarily Unix and its various, hybrid incarnations (esp. Linux flavors). The kit suffix refers to either: (a) the individual program mechanism or, (b) a collective of interoperative or interactive mechanisms designed to perform a set of predefined (encoded) tasks. In essence, one part of the kit may initiate the actual entry into the target / host computer system while another part of the rootkit mechanism will act to modify the same process for later, and more simplified means of access (and almost exclusively, surreptitiously).

Source: http://en.wikipedia.org/wiki/Rootkit