The autopilot is as an essential component of an UAV to execute the automatic flight control activities. An autopilot should be able to: 1. Measure flight parameters; 2. Process data; 3. Make decisions; 4. Create commands; all of these activities are performed via a microcontroller. The physical heart of an UAV autopilot is based in the microcontroller. This chapter presents the fundamentals of microcontroller; and how to setup a microcontroller to perform various functions of an autopilot. In the end, multiple open-source single-board microcontrollers are briefly introduced.