The high prevalence of chronic inflammatory oropharyngeal pathologies and a large variety of specific pathogenetic features of the persistent viral infections caused by the species of the families Herpesviridae and Papillomaviridae as etiological agents of the disease suggest the necessity of investigations with a view to evaluating the clinical significance of persistent viral infections with Herpesviridae and Papillomaviridae species in the patients presenting with chronic inflammatory oropharyngreal pathology. The objective of the present study was to elucidate the prevalence and clinical significance of viral infections caused by the pathogenic agents belonging to the families Herpesviridae and Papillomaviridae in the patients presenting with chronic inflammatory pathology of the oropharynx. We examined two groups of patients one of which was comprised of 174 subjects suffering from chronic inflammatory oropharyngeal pathologies while the other consisted of 31 healthy people. All the patients in both groups underwent the general clinical examination, real-time PCR diagnostics of the viral infections with Herpes viridae and Papilloma viridae using the scrapings of oropharyngeal mucosa, and the microbiological study of the oropharynx secretion. The study has demonstrated the high frequency of viral infections caused by Herpesviridae and Papillomaviridae species in the patients with chronic inflammatory pathology of the oropharynx in comparison with the control group of healthy subjects (81.03% and 45.16% respectively). It was shown that the certain types of pathological conditions were specifically associated with the concrete forms of viral infections. The results of the cytological study give evidence that all (100%) the patients with chronic inflammatory oropharyngeal pathologies had the specific changes in epithelium in the combination with the non-specific alterations. 63.6% of the patients with chronic inflammatory oropharyngeal pathologies and negative results of viral diagnostics using the real-time PCR technology were found to have non-specific changes in epithelium as opposed to 25.8% of the healthy subjects. The correlation analysis of the results of real-time PCR diagnostics and the bacteriological study showed that 45.1% of the carriers of the Epstein—Barr virus were infected with S. pneumoniae and 23.2% with Kl..pneumoniae whereas the mixed infection was documented in 31.1% of the EBV carriers. Moreover, 10.98% of such patients presented with Candida albicans infection whereas. 54.5% and 27.3% of the patients with HHV-6 were diagnosed as having S. aureus and S. pneumoniae infection respectively; the combined flora was found in 18.2% of such patients.