The aim of the study was to examine the use of histological methods of qualitative and quantitative evaluation of the deposition of newly created bone after endodontic therapy of chronic apical periodontitis in an experimental dog model. The pulp chambers of two animals (six roots each) were exposed to the effects of oral microflora. Endododontal therapy was performed after 35 days by ProFile® Ni-Ti rotating instruments and Thermafill® obturators, and the cavities filled with amalgam. One animal then received intraperitoneal injection of 100 mg/kg vital stain Procion Red and the other 10 mg/kg doxicyclin perorally for a period of 12 days. After 35 days of endodontic therapy the animals were sacrificed and qualitative and quantitative analysis performed on the histological specimens. Analysis of the newly deposited osteoid was possible by quantitative analysis of the specimens stained with toluidine blue. Analysis of mineralised newly created bone on the native specimens was enabled by analysis of the fluorescent deposits of Procion Red and oxycycline. Quantitative histomorphometric analysis demonstrated greater potential for healing lesions in the animal in which doxycycline was used for demarcation of newly created bone, compromising doxycycline as an independent marker.