Howtoforge posted a guide about configuring AIDE (Advanced Intrusion Detection Environment)

A file integrity scanner is something you need to have. Imagine a hacker placing a backdoor on your web site, or changing your order form to email him a copy of everyone's credit card while leaving it appear to be functionally normally.

By setting up daily reporting, this notifies you within, at most, 24 hours of when any file was changed, added, or removed. It also helps establish an audit trail in the event your site is compromised.

These instructions are designed for an end user, where you don't need to have root access, to implement and assumes your server has the aide binary installed. Most hosts will have this installed already, or will install it for you upon request.

  How To Configure The AIDE (Advanced Intrusion Detection Environment) File Integrity Scanner For Your Website