This paper presents development and performance analysis of an indoor low-cost motion tracking system for miniature Unmanned Aerial Vehicles. The proposed system is based on infrared markers embedded on the vehicle, the positions of which are captured in real time by Wiimote infrared cameras. Using at least two of these cameras, vehicle 3D position and orientation can be determined. Implementation of system hardware architecture developed as student research project in academic environment is discussed with its own limitations. Estimation method is presented. System performance analysis is also proposed, addressing optimization of detection area, accuracy and dispersion of measurements, and robustness with respect to outliers and hardware parameters. Experimental results are provided to illustrate system performance and to demonstrate satisfaction of imposed strict constraints for reliable motion tracking of a miniature UAV.