The measurement of peri-implant marginal bone loss is currently carried out using digital methods of radiographic analysis assisted by various types of software. The purpose of this study was to compare the characteristics of three different softwares: specific radiology software for the development and visualization of radiological images in DICOM format (3Dicom Viewer®), advanced level software for professional editing of bitmap images (or raster graphics) (Adobe Photoshop®), and mid-level software for processing bitmap-type images, programmed in Java and in the public domain (ImageJ®). It was verified that the three softwares used are valid for the measurement of peri-implant marginal bone loss provided that the appropriate protocol is fulfilled. The results showed no significant differences between Adobe Photoshop® and ImageJ® with respect to 3Dicom Viewer® in the measurements of mesial and distal bone loss of the implants, without influence of the dental sector where they were located. The measurements made with ImageJ® looked more like those of the control software (3Dicom Viewer®) than those of Adobe Photoshop®, but with a greater degree of dispersion. Thus, Adobe Photoshop® is a slightly inaccurate method but with less dispersion.