This paper describes a methodology to extract aerial vehicles' aerodynamic characteristics from visually tracked trajectory data. The technique is being developed to study the aerodynamics of centimeter-scale aircraft and develop flight simulation models. Centimeter-scale aircraft remains a largely unstudied domain of aerodynamics, for which traditional techniques like wind tunnels and computational fluid dynamics have not yet been fully adapted and validated. The methodology takes advantage of recent progress in commercial, vision-based, motion-tracking systems. This system dispenses from on-board navigation sensors and enables indoor flight testing under controlled atmospheric conditions. Given the configuration of retro-reflective markers affixed onto the aerial vehicle, the vehicle's six degrees-of-freedom motion can be determined in real time. Under disturbance-free conditions, the aerodynamic forces and moments can be determined from the vehicle's inertial acceleration, and furthermore, for a fixed-wing vehicle, the aerodynamic angles can be plotted from the vehicle's kinematics. By combining this information, we can determine the temporal evolution of the aerodynamic coefficients, as they change throughout a trajectory. An attractive feature of this technique is that trajectories are not limited to equilibrium conditions but can include non-equilibrium, maneuvering flight. Whereas in traditional wind-tunnel experiments, the operating conditions are set by the experimenter, here, the aerodynamic conditions are driven by the vehicle's own dynamics. As a result, this methodology could be useful for characterizing the unsteady aerodynamics effects and their coupling with the aircraft flight dynamics, providing insight into aerodynamic phenomena taking place at centimeter scale flight.