Abstract-This paper presents the Santa Cruz Low-Cost UAV GNC Subsystem (SLUGS) developed at the University of California Santa Cruz. It is a versatile and flexible autopilot capable of controlling a small unmanned system. It is tightly integrated with MATLAB/Simulink, and allows for a simple and easy transition from pure simulation to HIL simulation to flight code. The hardware's main processing units are two lowcost dsPIC33F DSCs, one handling sensor input and the other managing the navigation and control loops. The sensor DSC implements a complementary attitude and position filter. An interprocessor communication protocol delivers fused attitude and position estimates to the control DSC. The control DSC implements low-level platform stabilization using PID loops, and higher level waypoint following based on a line-of-sight guidance law. Data is logged and available for replay post flight on both the ground station software, and also within MATLAB/Simulink. The hardware was installed on a low-cost single engine electric RC aircraft, and has been demonstrated to be capable of sustained autonomous flight. Several estimation topologies have been tested and developed using the system. The SLUGS is general, and can be adapted to multiple autonomous platforms such as helicopters, quadrotors, twin engine aircraft, ground, and marine surface vehicles.