Three Tools to Scan a Linux Server for Malware and Rootkits

Servers connected to the internet are seeing a constant level of attacks and scans all day. While a firewall and regular system updates are a good first defense to keep the system safe, you should also check regularly that no attacker got in. The tools described in this tutorial are made for these sanity checks, they scan for malware, viruses, and rootkits. They should be run regularly, e.g. every night and send reports to you by email. You can also use Chkrootkit, Rkhunter, and ISPProtect to scan a system when you see suspicious activity like high load, suspicious processes or when the server suddenly starts to send malware.

All these scanners have to be run as root user. Login as root before you continue or run "sudo su" on Ubuntu to become root user.

chkrootkit - Linux Rootkit Scanner

Chkrootkit is a classic rootkit scanner. It checks your server for suspicious rootkit processes and checks for a list of known rootkit files.

Either install the package that comes with your distribution (on Debian and Ubuntu you would run

apt-get install chkrootkit

Install chkrootkit with apt

), or download the sources from and install manually:

wget --passive-ftp
tar xvfz chkrootkit.tar.gz
cd chkrootkit-*/
make sense

Download and Install Chkrootkit

Afterwards, you can move the chkrootkit directory somewhere else, e.g. to /usr/local/chkrootkit:

cd ..
mv chkrootkit-<version>/ /usr/local/chkrootkit

and create a symlink for easy access:

ln -s /usr/local/chkrootkit/chkrootkit /usr/local/bin/chkrootkit

To check your server with chkrootkit, run the command:


A common false positive report is:

Checking `bindshell'...                                     INFECTED (PORTS:  465)

Don't worry when you get this message on an email server, this is the SMTPS (Secure SMTP) port of your mail system and a well known false positive.

You can even run chkrootkit by a cron job and get the results emailed to you. First, find out the path where chkrootkit is installed on your server with:

which chkrootkit


[email protected]:/tmp/chkrootkit-0.50# which chkrootkit

Chkrootkit is installed in the path /usr/sbin/chkrootkit, we need this path in the cron line below:


crontab -e

To create a cron job like this:

0 3 * * * /usr/sbin/chkrootkit 2>&1 | mail -s "chkrootkit output of my server" [email protected])

That would run chkrootkit every night a 3:00h. Replace the path to chkrootkit with the one that you got from which command above and exchange the email address with your real address.

Lynis - Universal Security Auditing Tool and Rootkit Scanner

Lynis (formerly rkhunter) is a security auditing tool for Linux and BSD based systems. It performs a detailed auditing of many security aspects and configurations of your system. Download the latest Lynis sources from

cd /tmp
tar xvfz lynis-2.6.1.tar.gz
mv lynis /usr/local/
ln -s /usr/local/lynis/lynis /usr/local/bin/lynis

Install Lynis security scanner

This will install Lynis to the directory /usr/local/lynis and creates a symlink for easy access. Now run

lynis update info

to check if you use the latest version.

Now you can scan your system for rootkits by running:

lynis audit system

Lynis will perform a few checks and then stops to give you some time to read the results. Press [ENTER] to continue with the scan.

Lynis Scan started

At the end, it will show you a summary of the scan.

Lynis security scan result

To run Lynis non-interactively, start it with the --quick option:

lynis --quick

To run Lynis automatically at night, create a cron job like this:

0 3 * * * /usr/local/bin/lynis --quick 2>&1 | mail -s "lynis output of my server" [email protected])

This will run Lynis every night a 3:00h. Replace the email address with your real address.

ISPProtect - Website Malware Scanner

ISPProtect is a malware scanner for web servers, it scans for malware in website files and CMS systems like Wordpress, Joomla, Drupal etc. If you run a web hosting server, then the hosted websites are the most attacked part of your server and it is recommended to do sanity checks on them regularly. ISPProtect contains 5 scanning engines:

  • Signature-based malware scanner.
  • Heuristic malware scanner.
  • A scanner to show the installation directories of outdated CMS systems.
  • A scanner that shows you all outdated WordPress plugins of the whole server.
  • A database content scanner which checks MySQL databases for potentially malicious content.

ISPProtect is not free software, but there is a free trial that can be used without registration to test it or clean an infected system.

ISPProtect requires PHP and clamav to be installed on the server, this should be the case on most hosting systems. ClamAV is used by ISPProtect in the first scan level with ISPProtect's own Malware signature set. In case you don't have a command line PHP installed yet, execute:

apt-get install php5-cli clamav

on Debian or Ubuntu or:

yum install php

on Fedora and CentOS.

Run the following commands to install ISPProtect.

mkdir -p /usr/local/ispprotect
chown -R root:root /usr/local/ispprotect
chmod -R 750 /usr/local/ispprotect
cd /usr/local/ispprotect
tar xzf ispp_scan.tar.gz
rm -f ispp_scan.tar.gz
ln -s /usr/local/ispprotect/ispp_scan /usr/local/bin/ispp_scan

To start ISPProtect, run:


The scanner automatically checks for updates, then asks for the key (enter the word "trial" here) and then asks for the path of the websites, normally that's /var/www.

ISPProtect Website Malware scanner started

Please enter scan key: <-- trial
Please enter path to scan: <-- /var/www

The scanner will now start the scan. The scanning progress is shown. The names of the infected files are shown on the screen at the end of the scan and the results are stored in file sin the ISPProtect install directory for later use:

After the scan is completed, you will find the results also in the following files:
Malware => /usr/local/ispprotect/found_malware_20180127115005.txt
Wordpress => /usr/local/ispprotect/software_wordpress_20180127115005.txt
Joomla => /usr/local/ispprotect/software_joomla_20180127115005.txt
Drupal => /usr/local/ispprotect/software_drupal_20180127115005.txt
Mediawiki => /usr/local/ispprotect/software_mediawiki_20180127115005.txt
Contao => /usr/local/ispprotect/software_contao_20180127115005.txt
Magentocommerce => /usr/local/ispprotect/software_magentocommerce_20180127115005.txt
Woltlab Burning Board => /usr/local/ispprotect/software_woltlab_burning_board_20180127115005.txt
Cms Made Simple => /usr/local/ispprotect/software_cms_made_simple_20180127115005.txt
Phpmyadmin => /usr/local/ispprotect/software_phpmyadmin_20180127115005.txt
Typo3 => /usr/local/ispprotect/software_typo3_20180127115005.txt
Roundcube => /usr/local/ispprotect/software_roundcube_20180127115005.txt
Shopware => /usr/local/ispprotect/software_shopware_20180127115005.txt
Mysqldumper => /usr/local/ispprotect/software_mysqldumper_20180127115005.txt
Starting scan level 1 ...
Scanning 3471 files now ...

To run ISPProtect automatically as a nightly cronjob, create a cron file with nano:

nano /etc/cron.d/ispprotect

and insert the following line:

0 3  * * *   root	/usr/local/ispprotect/ispp_scan --update && /usr/local/ispprotect/ispp_scan --path=/var/www [email protected] --non-interactive --scan-key=AAA-BBB-CCC-DDD

Replace "[email protected]" with your email address, the scan report is sent to this address. Then exchange "AAA-BBB-CCC-DDD" with your license key. You can get a license key here.

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15 Comment(s)

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From: Randy Thompson at: 2016-02-14 18:43:37

Nothing on clamav?

From: Warren at: 2016-02-14 23:17:53

ISPProtect requires clamav to be installedapt-get install clamavI've also found rkhunter useful. Ubuntu: apt-get install rkhunter

Redhat / CentOS: cd /tmpwget -xzvf rkhunter-1.4.2.tar.gzcd rkhunter-1.4.2./ --layout default --installUpdate:rkhunter --updaterkhunter --propupd


Scan:rkhunter --checkScan without Prompts:rkhunter --check --skip-keypress

From: till at: 2016-02-15 08:50:43

The software Lynis that I covered above is the new software from the author of rkhunter. As far as I can see, it includes the rkhunter functionality and replaces it.

From: Warren at: 2016-02-15 22:39:50

Good to know Thank you :)

From: Warren at: 2016-02-15 00:14:34

Unhide is also usefulUbuntu: apt-get install unhideRedhat/CentOS: yum install unhide

Compile Manually:

#pre-requisitesyum install gccyum install glibc-static

#downloadcd /tmpwget -zxvf unhide-20121229.tgzcd unhide-20121229

#compilegcc -Wall -O2 --static -pthread unhide-linux*.c unhide-output.c -o unhide-linuxgcc -Wall -O2 --static unhide-tcp.c unhide-tcp-fast.c unhide-output.c  -o unhide-tcp

#create symbolic linkcp unhide-linux unhide-tcp /usr/local/bin && cd /usr/local/bin/ && ln -s unhide-linux unhide

#helpunhide -h

#scanunhide -f sysunhide -f procunhide-tcp

From: Warren at: 2016-02-15 22:39:14

I'm not sure why all my spacing is wrong...Try this again;


ISPProtect requires clamav to be installed

apt-get install clamav


I've also found rkhunter useful. 

Ubuntu: apt-get install rkhunter


Redhat / CentOS: 

cd /tmp


tar -xzvf rkhunter-1.4.2.tar.gz

cd rkhunter-1.4.2

./ --layout default --install



rkhunter --update

rkhunter --propupd



rkhunter --check


Scan without Prompts:

rkhunter --check --skip-keypress



Unhide is also useful

Ubuntu: apt-get install unhide

Redhat/CentOS: yum install unhide


Compile Manually:

yum install gcc

yum install glibc-static

cd /tmp


tar -zxvf unhide-20121229.tgz

cd unhide-20121229

gcc -Wall -O2 --static -pthread unhide-linux*.c unhide-output.c -o unhide-linux

gcc -Wall -O2 --static unhide-tcp.c unhide-tcp-fast.c unhide-output.c  -o unhide-tcp

cp unhide-linux unhide-tcp /usr/local/bin && cd /usr/local/bin/ && ln -s unhide-linux unhide



unhide -h



unhide -f sys

unhide -f proc


From: Liam at: 2016-10-21 07:04:34

Thanks for mentioning unhide. Nice tool!

From: Jesse Norell at: 2016-05-12 22:53:51

If you install chkrootkit from debian package, it comes with a cronjob already, just set RUN_DAILY="true" in /etc/chkrootkit.conf.

From: tilaris at: 2016-07-24 17:41:54


for the new lynis

From: Arounan at: 2016-08-30 17:50:34


for the new lynis

From: Mr. Mister at: 2016-12-16 16:33:55

Well done my friend. Very helpful and useful article.

From: danish at: 2017-03-27 12:41:30

great one brah. very helpful

From: felan at: 2017-04-09 17:28:25

lynis is avalable in Debian repo. And the syntax I had to use was lynis --auditor system and not lynis audit system. Just a little info :)

From: Jeff Huckaby at: 2017-05-04 14:21:50

No tool or set of tools is 100% complete. For better rookits, they can avoid detection by all of these tools. 

With RPM based systems, you can use rpm -V to verify a package against its manifest.    You can also use md5sum and compare binaries to known good ones.  

Also you can never trust even the most basic commands when working on a potentially rooted system.  If taking the server offline is not a possibility, then I recommend using statically compiled tools.  This way you can assure that the libs things like bash, lsof, ps and others link into are not hacked.   

For simpler rootkits often used by botnets, I find they often set the immutable bit on files in *bin directories.  You can easily check this using lsattr and look for s - i -a attributes in tools like ps, find etc. 


From: felan at: 2018-02-03 21:25:44

Linux Malware Detection is also worth looking in to. There are scripts on here to install it on debian/ubuntu, but here is a link to their website: