The aim of this research was to compare different methods of geometric alignment produced by two programs developed to be utilized for digital subtraction radiography (DSR). Material and Methods: Material consists of 50 pairs of intra-oral radiographs taken in 50 patients during normal oral clinical treatment. Two programs invented by the authors of this article: ToothVis 1.4 (TV) and DentalStudio 2.0 (DS) software were used in this study. Images obtained by two methods of DSR (cut and divide) and geometrically aligned with four methods were compared with the use of the peak signal to noise ratio (PSNR). Results: Analyzing the PSNR, it was observed that for cut subtraction its values ranged from 37.93 dB to 39.99 dB. For divide subtraction the PSNR values varied between 39.00 dB (03_pt_DS vs 10_pt_TV) and 47.73 dB (03_pt_TV vs 10_pt_TV). The PSNR achieved higher values for divide than for cut subtraction. Comparing cut and divide subtraction, the PSNR was the lowest for 3-point geometric alignment. Conclusion: Geometric alignment with the ToothVis software combined with divide subtraction gives the best quality of a subtracted image.