Either with chkrootkit or with rkhunter.

chkrootkit

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

apt-get install chkrootkit

), or download the sources from www.chkrootkit.org and install manually:

wget --passive-ftp ftp://ftp.pangeia.com.br/pub/seg/pac/chkrootkit.tar.gz
tar xvfz chkrootkit.tar.gz
cd chkrootkit-<version>/
make sense

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

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

Now you can run chkrootkit manually:

cd /usr/local/chkrootkit
./chkrootkit

(if you installed a chkrootkit package coming with your distribution, your chkrootkit might be somewhere else).

You can even run chkrootkit by a cron job and get the results emailed to you:

Run

crontab -e

to create a cron job like this:

0 3 * * * (cd /usr/local/chkrootkit-<version>; ./chkrootkit 2>&1 | mail -s "chkrootkit output my server" you@yourdomain.com)

That would run chkrootkit every night a 3.00h.

rkhunter

Download the latest rkhunter sources from www.rootkit.nl:

wget http://downloads.rootkit.nl/rkhunter-1.2.7.tar.gz
tar xvfz rkhunter-1.2.7.tar.gz
cd rkhunter/
./installer.sh

This will install rkhunter to the directory /usr/local/rkhunter. Now run

rkhunter --update

to download the latest chkrootkit/trojan/worm signatures (you should do this regularly).

Now you can scan your system for malware by running

rkhunter -c