The objective of the present work was to develop the standardized approaches to pharmacotherapy of chronic tonsillitis based on the data of regional specificity of the tonsillar microflora. The methods of investigations included the study of throat swabs obtained from 668 patients presenting with various forms of chronic tonsillitis (CT). Half of these patients were shown to be infected with Streptococcus pyogenes and 24.5% with Mycoplasma pneumoniae. The presence of concomitant pathology of the respiratory and digestive tracts in the patients with CT increases the probability of identification of enterobacteria, enteroccocci, and staphylococci in combination with streptococci and mycoplasmas. It is concluded that the choice of antibacterial therapy should be based on the results of analysis of the aggravated medical history and bacteriological diagnostics including the isolation of all putative pathogens and examination of their susceptinility to antibacterial agents.