This paper presents a low-cost 6 Degrees-of-Freedom (6 DoF) visual tracking technique and its system for a small indoor rotary-wing Unmanned Aerial Vehicle (UAV) using three onboard LEDs and a single on-ground camera. The ellipse formed by the cyan LEDs on the blades and the red LED in the captured image are utilised for pose estimation. The developed system successfully implements the proposed technique with a sampling rate of 9-12Hz. The most notable contributions of this paper are the novel configuration of the LEDs for visual tracking using only three LEDs and one camera for 6 DoF motion tracking of a UAV and the wide range of observable flight. The experimental results show 1-3% percentage error in the developed system at various ranges, directions and vehicle velocities in an indoor environment, demonstrating the effectiveness of the proposed technique.