The request for very accurate 3D reconstruction in several applications is leading to the development of very large motion capture systems. A good synchronization of all the cameras in the system is of fundamental importance to guarantee the effectiveness of the 3D reconstruction. In this work, first, an approximation of the reconstruction error variance taking into account of synchronization errors is derived. Then, a Kalman filter approach is considered to estimate the cameras synchronization errors. The estimated delays can be used to compensate the synchronization error effect on the reconstruction of target positions. The results obtained in some simulations suggest that the proposed strategy allows to obtain a significant reduction of the 3D reconstruction error.