Installation Rootkit Hunter (rkhunter) on CentOS 5 and 6

Rootkit Hunter (rkhunter) is a Unix-based tool that scans for rootkits, backdoors and possible local exploits. This guide explains how to install and configure RKHunter on CentOS 5,6 or 7.

Rootkits are self-hiding toolkits secretly installed by a malicious intruder to allow that user to gain access to the server. Rootkit Hunter offers protection by comparing SHA-1 hashes of important files with known good ones in a online database as well as:

    • MD5 hash compare
    • Look for default files used by rootkits
    • Wrong file permissions for binaries
    • Look for suspected strings in LKM and KLD modules
    • Look for hidden files
    • Optional scan within plaintext and binary files

Note: This guide assumes you are familiar with SSH and basic command line navigation. These instructions apply primarily to customers who have Virtual Private Servers or Dedicated servers. If you do not have root-level access you will not be able to make these changes.

1. Installation

1.1 Install EPEL Repository

All files required for installation of RKHunter are contained in the EPEL repository.

yum install epel-release

If this command does not work, perhaps because the CentOS Extras repository is disabled, the section below provides manual installation instructions based on your distribution version.

CentOS and Red Hat Enterprise Linux 5.x

wget sudo rpm -Uvh epel-release-5*.rpm

CentOS and Red Hat Enterprise Linux 6.x

wget sudo rpm -Uvh epel-release-6*.rpm

CentOS and Red Hat Enterprise Linux 7.x

wget sudo rpm -Uvh epel-release-7*.rpm

If you get a File Not Found error message when trying to download the package, the version number might have changed. You can access the latest version of the RPM installer from the Fedora EPEL wiki page. The wiki page also includes additional instructions for Red Hat Network subscribers who are installing the EPEL repository.

1.2 Installation Rootkit Hunter

Once the EPEL Repository has been installed, issue the following command as root to start the installation routine.

yum -y install rkhunter

1.3 Update Database

rkhunter --update

1.4 Update system file properties

This is a necessary step to establish a foundation database file to compare scans. On a clean install, the first run of propupd, creates a new database file. On later scans, running the propupd command, updates the database file. So, to update the database file, you are satisfied you have only trusted source system file changes. RKHunter offers choices, in the CONF, in how you verify system file changes.

rkhunter --propupd

2. Automate Rootkit Hunter

Rkhunter can be setup to run checks every day so that we always have up-to-date information about intrusions. This can be accomplished by creating a cronjob.

Note: More recent versions of RKHunter have a cronjob preinstalled under the /etc/cron.daily directory. In this case steps 2.1, 2.2 and 2.3 can be ignored.

2.1 Create Cron File

Create the run-file in the following location (RHEL based distributions only):

nano -w /etc/cron.daily/

2.2 Insert Shell Script

The script below can be configured to send email notifications to a specified email id. The --versioncheck checks our threat definitions are up to date. The --update option updates our threat definitions, if required. The --cronjob option tells rkhunter to not require interactive key presses. You need to insert this short shell script to the file we have just created.

/usr/local/bin/rkhunter --versioncheck
/usr/local/bin/rkhunter --update
/usr/local/bin/rkhunter --cronjob --report-warnings-only
) | /bin/mail -s 'rkhunter Daily Scan Report (PutYourServerNameHere)'

Important: Remember to change: (PutYourServerNameHere) AND to a valid server name / e-mail address

2.3 Set Execute Permissions

Set execute permission on the file you have just created:

chmod 755 /etc/cron.daily/

The cron utility will run once daily, and if a threat is detected, the rkhunter command itself will email our user to alert them. If no problems were found, no email will be received.

3. Rootkit Hunter configuration

The configuration file for rkhunter can be found at:


3.1 Setup Mail Notifications

E-mail notifications can be enabled by editing the MAIL-ON-WARNING value as below. You will then receive a message when rkhunter hits a warning.


3.2 SSHD Root Logon

The parameter ALLOW_SSH_ROOT_USER tells rkhunter whether or not the root user is allowed to ssh into the system. This is unset by default in the rkhunter.conf file. Rkhunter will complain about this on every run. If you have disabled root login, you should set this parameter to "no".


If you need root login over SSH, you should change this parameter to "yes" so that rkhunter can check this and will mark this setting as valid:


Security practices recommend disabling root login.

3.3 Whitelist known scripts

The SCRIPTWHITELIST parameter can be set to tell rkhunter that these are expected, known to be safe files. This will prevent these files from triggering false positives on all subsequent checks.


4. Update rkhunter

To check the currently installed version enter the following:

# rkhunter --versioncheck

Run the updater by issuing the following command:

# rkhunter --update

With our database files refreshed, we need to tell rkhunter to check the current values and store them as known-good values:

# rkhunter --propupd


5. Manual Scan

You can initiate a manual scan by issuing the following command:

rkhunter -c 

Which runs rkhunter in interactive mode. In other words, when it gets to the end of a particular scan, you need to press 'enter' to continue. If you want to "auto skip" interactive mode, add the -sk option at the end:

rkhunter -c -sk

Alternatively the --check flag may be used:

rkhunter --check -sk


Your scan results should look as follows:

---------------------------- Scan results ----------------------------
MD5 scan
Scanned files: 0
Incorrect MD5 checksums: 0
File scan
Scanned files: 412
Possible infected files: 0
Application scan
Vulnerable applications: 0
Scanning took 39 seconds

6. rkhunter help

For more information and options please run the following command.

# rkhunter --help

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