Organizing Code in Web Develpment [on hold]

this is my first post on Stack Overflow so treat me well ;).

I've been using php to organize my code for quite a while now, and by this I mean I have separate php folders for things such as my navigation, footer etc and then just include that specific file in the correct spot to save me having to insert the whole chunk of code again.

From a organization point of view, I like this method as it's also a lot cleaner, but how does this change things in terms of performance of the website?

Thanks, Cameron