In order to successfully perform the 3D reconstruction in electron tomography, transmission electron microscope images must be accurately aligned or registered. So far, the problem is solved by either manually showing the corresponding fiducial markers from the set of images or automatically using simple correlation between the images on several rotations and scales. The present solutions, however, share the problem of being inefficient and/or inaccurate. We therefore propose a method in which the registration is automated using conventional colloidal gold particles as reference markers between images. We approach the problem from the computer vision viewpoint; hence, the alignment problem is divided into several subproblems: (1) finding initial matches from successive images, (2) estimating the epipolar geometry between consecutive images, (3) finding and localizing the gold particles with subpixel accuracy in each image, (4) predicting the probable matching gold particles using the epipolar constraint and its uncertainty, (5) matching and tracking the gold beads through the tilt series, and (6) optimizing the transformation parameters for the whole image set. The results show not only the reliability of the suggested method but also a high level of accuracy in alignment, since practically all the visible gold markers can be used.