MD5 hash check is a basic Joomla Security tool for a little security checks over all your Joomla files and 3rd party extensions. This tool will let you scan through all your Joomla files and make sure that all the files are valid and same as extracted from the original zip file downloaded from Joomla.org (joomlacode.org) It will also tell you if any core Joomla files are missing.
I wrote to the hosting company in wich servers the hackers were where based (I discovered so many things on their hidden places, you wouldn't beleive!!!) And guess what? - I never received even an appology from that company!
So, I had to start my website entirely from the beginning.
Now I use several ways to protect the code and MD5 Comparison Toolis one of them. It is easy to use and it gives you a priceless helping hand when you want to look a bit deeper.
this tool at the first shot itself gave us a list of file which have been modified and we didn't overwrite those files.