The chkrootkit security scanner searches for signs that the system is infected with a 'rootkit'. Rootkits are a form of malware that seek to exploit security flaws to grant unauthorised access to a computer or its services, generally for malicious purposes.
chkrootkit can identify signs of over 70 different rootkits (see the project's website for a list).
Please note that an automated tool like chkrootkit can never guarantee a system is uncompromised. Nor does every report always signify a genuine problem: human judgement and further investigation will always be needed to assure the security of your system.