Background and aim The aim of our study was to analyze the correlations between pharyngeal bacterial flora and middle ear (ME) changes in children with otitis media (OM). Material and Methods A total of 259 children at the age of 3 – 4 years with OM were involved in our prospective study which included microbiological test from nasopharynx, standard treatment (medical and surgical) and otomicroscopical, functional examinations of ears and charts analysis in 5 years after surgery. All children were divided on 4 groups according to the OM outcome. Results The most complicated outcome of OM with the formation of chronic suppurative and adhesive forms was registered in children with Str. beta-hemolytic pyogenes presented in pharynx in early childhood. Majority of these patients (87%) underwent ear surgery for more than 2 times due to chronicity. Otomicroscopy revealed that tympanic membrane is gray, thin, retracted, with adhesions. In middle ear we noted presence of granulations, polyps, viscous, thick effusion and cholesteatoma. Relatively benign OM evolution was registered in children with Str. pneumoniae and Staph. aureus in pharynx; usually it was necessary one surgical treatment. Otomicroscopy revealed that tympanic membrane is thicker, with good vascularization. In middle ear we noted presence of mucous effusion and thick mucosa. Children with Moraxella catarrhalis and Haemophilus influenzae in pharynx in the majority of cases were successfully treated by medical methods. Only in 15% of cases we made surgical treatment in that group. Conclusion The pharyngeal microbial flora in children with OM influences on further evolution of the middle ear pathology. Children with Streptococcus beta-hemolytic pyogenes and OM have to be on close observation, need early comprehensive treatment including surgical one.