Determination of reference points is a precondition for reconstruction of serial sections. In the case of comprehensive reconstruction work, manual extraction of the markers may be very time-consuming and may even make such reconstruction impossible. The procedure presented in this contribution allows automatic alignment of histological preparations provided that nuclei or comparable structures extend over several sections and are capable of being extracted using methods of pattern recognition. The method was applied to 50 sections with Nissl staining. The nuclei were extracted from the images and evaluated by application of the algorithm. All image pairs were correctly aligned. An integrated control mechanism ensures automatic detection of incorrectly aligned images.