Introduction The dynamic study of the serotype composition and the level of antibiotic resistance of S. pneumoniae in different regions is the most important component of the control of pneumococcal infections (PI). The aim of the study was to analyze the serotype composition of S. pneumoniae isolated from the nasopharynx in children under 5 years of age, as well as to assess the sensitivity of pneumococci to antimicrobials, depending on the vaccination status and previous antibacterial therapy. Materials and methods A multicenter cohort study of nasopharyngeal carriage, serotype diversity and sensitivity to pneumococcal antibiotics were conducted in 13 centers in the Republic of Khakassia. Results 498 nasopharyngeal smears were collected, pneumococcus was isolated in 51.6% of cases. PI vaccination coverage in the cohort was 67.2%. The carriage of pneumococcus did not differ in children depending on their vaccination status (52.3% in vaccinated and 52.2% in unvaccinated). There was revealed a significant decrease in the carrier rate of pneumococcal vaccine serotypes in the cohort of vaccinated children compared with unvaccinated (17.6% vs 34.7%, p <0.05). High resistance of S. pneumoniae to penicillin (38.6%), macrolides (29.7%), trimethoprim/sulfamethoxazole (28.6%) was found. Amoxicillin resistance accounted for 20.8%, and ceftriaxone - 16.6%. Antibiotic-resistant vaccine serotypes were twofold more common. Conclusion The introduction of mass vaccination against PI in the country does not reduce the nasopharyngeal carriage of pneumococcus, but significantly reduces the circulation of vaccine serotypes, including strains resistant to antibiotics.