A root kit is a set of tools used by an intruder after cracking a computer system. These tools can help the attacker maintain his or her access to the system and use it for malicious purposes. Root kits exist for a variety of operating systems such as Linux, Solaris, and versions of Microsoft Windows.

The term "root kit" (also written as "rootkit") originally referred to a set of recompiled Unix tools such as "ps", "netstat", "w" and "passwd" that would carefully hide any trace of the cracker that those commands would normally display, thus allowing the crackers to maintain "root" on the system without the system administrator even seeing them.

Generally now the term is not restricted to Unix based operating systems, as tools that perform a similar set of tasks now exist for non-Unix operating systems such as Microsoft Windows (even though such operating systems may not have a "root" account). It is common for the term 'rootkit' to refer to a "kernel-mode" program (that is, acting as part of the operating system), as opposed to a "user-mode" program (that is, programs that operate as normal applications or tools).

The key distinction between a computer virus and a root kit relates to propagation. Like a root kit a computer virus modifies core software components of the system, inserting code which attempts to hide the "infection" and provides some additional feature or service to the attacker (the "payload" of a virus).

In the case of the root kit the payload may attempt to maintain the integrity of the root kit (the compromise to the system) --- for example every time one runs the root kit's ps command it may check the copies of init and inetd on the system to ensure that they are still compromised, and "re-infecting" them as necessary. The rest of the payload is there to ensure that the cracker (attacker) can continue to control the system. This generally involves having backdoors in the form of hard-coded username/password pairs, hidden command-line switches or magic environment variable settings which subvert the normal access control policies of the uncompromised versions of the programs. Some root kits may add port knocking checks to existing network daemons (services) such as inetd or the sshd

A computer virus can have any sort of payload. However, the computer virus also attempts to spread to other systems. In general a root kit limits itself to maintaining control of one system.

A program or suite of programs that attempts to automatically scan a network for vulnerable systems and to automatically exploit those vulnerabilities and compromise those systems is referred to as a computer worm. Other forms of computer worms work more passively, sniffing for usernames and passwords and using those to compromise accounts, installing copies of themselves into each such account (and usually relaying the compromise account information back to the cracker/attacker through some sort of covert channel).

Of course there are hybrids. A worm can install a root kit, and a root kit might include copies of one or more worms, packet sniffers or port scanners. Also many of the e-mail worms to which MS Windows platforms are uniquely vulnerable are commonly referred to as "viruses." So all of these terms have somewhat overlapping usage and can be easily conflated.

A number of new rootkit detection tools have been created including Blacklight (windows), rkhunter (unix/linux).