The reconstruction of a scene via a stereo-camera system is a two-steps process, where at first images from different cameras are matched to identify the set of point-to-point correspondences that then will actually be reconstructed in the three dimensional real world. The performance of the system strongly relies of the calibration procedure, which has to be carefully designed to guarantee optimal results. We implemented three different calibration methods and we compared their performance over 19 datasets. We present the experimental evidence that, due to the image noise, a single set of parameters is not sufficient to achieve high accuracy in the identification of the correspondences and in the 3D reconstruction at the same time. We propose to calibrate the system twice to estimate two different sets of parameters: the one obtained by minimizing the reprojection error that will be used when dealing with quantities defined in the 2D space of the cameras, and the one obtained by minimizing the reconstruction error that will be used when dealing with quantities defined in the real 3D world.