||Streptococcus pneumoniae nfection is a serious public health concern in the world, especially among infants and young children. Data on S.pneumoniae carriage rate, incidence of pneumococcal disease, serotype distribution and resistance to antimicrobials in Lithuania are limited. The aim of the research was to evaluate S.pneumoniae nasopharyngeal colonisation in preschool children and its influence on the course of acute respiratory tract infections. The prospective study was carried out in five cities from all main regions of the country from February 2012 to March 2013. A total of 900 children were included. S.pneumoniae nasopharyngeal colonisation rate was high (40.8%) in preschool children with acute respiratory tract infections. The most prevalent S.pneumoniae serotypes (6A, 6B, 14, 15, 19F and 23F) in Lithuania were the same ones that had been predominant in other European countries before introduction of pneumococcal vaccines into national immunisation programme. S.pneumoniae nasopharyngeal colonisation had a negative impact on the course of acute respiratory tract infections (longer recovery duration, longer absent from day-care centres, higher rates of acute otitis media, bronchitis and pneumonia, more frequent use of antimicrobials). Most S.pneumoniae strains were sensitive to commonly used antimicrobials (e.g., penicillin, macrolides). Currently commercially available pneumococcal conjugate vaccines could be effective for children in Lithuania.