In cone-beam tomography, relatively small misalignment of the imaging system is geometrically magnified and may cause severe distortion of the reconstructed image. We describe a method for alignment of a cone-beam tomography system built on an x-ray microfocus tube, an image intensifier, and a high-resolution CCD camera. To obtain geometrical parameters of system misalignment, we suggest measuring two 180-deg-opposed cone-beam radiographs of a specially manufactured calibration aperture. An advantage of the aperture over other calibration objects is that we can easily restore its idealized picture by applying a certain threshold to the measured data. The method permits the lateral displacement vector and lateral tilt angle to be accurately found. Unlike other alignment methods, our approach enables virtual system alignment by using mathematical processing of the measured data, rather than moving the parts of the system. The virtually aligned system data are used for 3-D image reconstruction by a standard filtered backprojection algorithm. Experimental results demonstrate considerable improvement of the image quality after applying the alignment method suggested. © 1999 Society of Photo-Optical Instrumentation Engineers.