In this paper, the design of a real-time image acquisition system for tracking the movement of Drosophila in three-dimensional space is presented. The system uses three calibrated and synchronized cameras to detect multiple flies and integrates the detected fly silhouettes to construct the three-dimensional visual hull models of each fly. We used an extended Kalman filter to estimate the state of each fly, given past positions from the reconstructed fly visual hulls. The results show that our approach constructs the three-dimensional visual hull of each fly from the detected image silhouettes and robustly tracks them at real-time rates. The system is suitable for a more detailed analysis of fly behaviour.