The objective of the study was to define treatment strategy in cases of facial bones bisphosphonate induced osteonecrosis based on the study of the role of conditionally pathogenic oral microorganisms. Three typical clinical cases of bisphosphonate osteonecrosis of the facial bones were analyzed and 15 conditionally pathogenic oral microorganisms were identified in these patients using real-time PCR in saliva, wound and bone samples. A comparative analysis was carried out with purulent-inflammatory diseases of maxillofacial area. The study results proved an important role of conditionally pathogenic microorganisms of the oral cavity in the development of osteonecrosis of the facial bones. Wide range of bacterial species was identified in osteonecrosis of the facial bones patients. While bone tissue is most exposed to microbial communities, surgical treatment results in effective rehabilitation for a long period.