Diversity in unmanned vehicle designs and control as well as diversity in existing autopilots lead to major compatibility issues among different platforms. The small number of different autopilot designs currently available in the market and their limitations, justifies the rationale for proposing design of a new modular, flexible, easy to integrate autopilot, suitable for multiple platforms. A discussion and comparison of the state of the art in autopilot research is presented, followed by the introduction of an autopilot design that will provide a novel and wellneeded processing platform for unmanned systems. The design is fully integrated with MATLAB/Simulink allowing for both simplified high level programming and hardwarein-the-loop capabilities, and provides a flexible FPGAbased platform that maximizes parallel processing and allows for analog signal conditioning that can be modified through digital communication from FPGA processor.