A file integrity program such as Tripwire protects against Trojan horse attacks by:

Tripwire generates a database of the most common files and directories on your system. Once it is generated, you can then check the current state of your system against the original database and get a report of all the files that have been modified, deleted or added. This comes in handy if you allow other people access to your machine and even if you don't, if someone else does get access, you'll know if they tried to modify files such as /bin/login etc.