uC Hobby has a piece up on the use of interrupt routines in Ardunio programming:

Often when working on microcontroller projects you need a background function to run at regular intervals. This is often done by setting up a hardware timer to generate an interrupt. The interrupt triggers an Interrupt Service Routine (ISR) to handle the periodic interrupt. In this article I describe setting up the 8-Bit Timer2 to generate interrupts on an Arduino ATMega168. I walk through steps required for setup and inside the ISR function.

Arduino Interrupts – Link