In this thesis, an architecture for the adaptive mode transition control of unmanned aerial vehicles (UAV) is presented. The proposed architecture consists of three levels: the highest level is occupied by mission planning routines where information about way points the vehicle must follow is processed. The middle level uses a trajectory generation component to coordinate the task execution and provides set points for low-level stabilizing controllers. The adaptive mode transitioning control algorithm resides at the lowest level of the hierarchy consisting of a mode transitioning controller and the accompanying adaptation mechanism. The mode transition controller is composed of a mode transition manager, a set of local controllers, a set of active control models, a set point filter, a state filter, an automatic trimming mechanism and a dynamic compensation filter. Local controllers operate in local modes and active control models operate in transitions between two local modes. The mode transition manager determines the actual mode of operation of the vehicle based on a set of mode membership functions and activates a local controller or an active control model accordingly. The adaptation mechanism uses an indirect adaptive control methodology to adapt the active control models. For this purpose, a set of plant models based on fuzzy neural networks is trained based on input/output information from the vehicle and used to compute sensitivity matrices providing the linearized models required by the adaptation algorithms. The effectiveness of the approach is verified through software-in-the-loop simulations, hardware-in-the-loop simulations and flight testing.