Inflammation of the pulp and periapical tissues is the main cause of tooth loss in patients worldwide, therefore endodontics is one of the most rapidly developing specialties in dentistry. Despite proper endodontic treatment, in many cases it is not possible to determine the etiology of infection or the reason for its relapse. Many research studies indicate that infections of the periapical tissues are mainly caused by strictly anaerobic bacteria. At present, more and more often the composition of the microflora within the inflammatory lesions is being evaluated with the use of molecular techniques, which showed that classical culture methods are not able to determine the etiology of infections of the periapical tissues. The results of these studies contributed to the major changes in our understanding of the microbiome composition in the endodontium. Purulent endodontic lesions are particularly important, as they may lead to many severe – even life-threatening – systemic complications.