Yes, the userspace tool is dependent on the kernel version of Netfilter installed along the lines of pppd and pcmcia-cs. You should install the userspace tools to different directories if you need multiple copies of the tool on your system. EG: Current --prefix=/ 2.4.20-20.9 --prefix=/usr/local/iptables/2.4.20-20.9 Then in your firewall scripts, you could have something like: if [ "`uname -v`" = "2.4.20-20.9" ]; then PREFIX="/usr/local/iptables/2.4.20-20.9" else PREFIX="/" fi IPTABLES=$PREFIX/bin/iptables $IPTABLES -P INPUT ... You could make it even more generic, but that is probably just overkill for what you are trying to solve.