Anti-virus software now scans for rootkits; a rootkit is a type of malware that is designed to gain administrative-level control over a computer system without being detected.
Rootkits can change how the operating system functions and in some cases, rootkits can tamper with the anti-virus program and render it ineffective.
Rootkits are also very difficult to remove, in some cases requiring a complete re-installation of the operating system.