The Delfly is subject of great interest from the aerodynamics department at the TU Delft. Current wind tunnel measurements are performed with a dual high speed camera setup that detect particles injected in the wind stream. The difference between two subsequent images provides information on the flow field around the wings of the Delfly. These measurements are always performed with the Delfly fixed on a support. Although this method produces a lot of useful data, the restrictions that the support introduces makes it not a true representation of the free flight conditions. This thesis goal therefore, was to design, build and test a system that would enable the Delfly to fly freely in the wind tunnel. This would allow the same measurements to be performed without a support, providing insight in the influence of the support on the aerodynamic properties of the Delfly. A low-cost, high performance tracking system using two Wiimotes was developed, providing 3D position information with an accuracy of 0.8 mm and a tracking rate up to 80 Hz. A custom auto pilot module was designed, containing a 3-axis gyro and an infrared camera. A small Bluetooth module provided two way communication between the Delfly and the ground station, allowing the position information to be sent up to the Delfly and can log the information from the on-board sensors. Using the tracking system and a LED in the middle of the wind tunnel to provide the camera with a heading reference, a PI controller was implemented on-board. The controller could successfully keep the Delfly within ±1.7 cm in forward and vertical direction, and within ±3.5 cm in lateral direction of the reference point. It is the first time in the world that a flapping wing micro aerial vehicle was flown autonomously in the wind tunnel. The achieved precision is sufficient for the aerodynamic measurements to be performed, which could shed more light on the way the wind tunnel support influences the properties of the Delfly. Furthermore, for the first time, good quality data has been gathered on the dynamic behavior of the Delfly. This can serve as a starting point for future projects, such as the design of more advanced controllers that cope with the observed non-linearities or provide a reference for future research on the dynamics of the Delfly