Rapid and accurate identification of Streptococcus pneumoniae is important for appropriate and prudent antimicrobial use in the treatment of lower respiratory tract infection. It is difficult to separate S. pneumoniae from commensal viridans group streptococci either by classical techniques or molecular methods. Aim of this study was to compare a commercially available multiplex PCR assay Seeplex PneumoBacter ACE Detection assay (Seegene, Seoul, South Korea), and in-house multiplex PCR using primer sets for lytA and cpsA for ability to differentiate S. pneumoniae in a known set of bacteria (S. pneumoniae and viridans group streptococci) and clinical samples. Of 20 viridans streptococcal isolates, 8 were misidentified as S. pneumoniae by commercial PCR test. Of 209 throat swabs tested with Seeplex PneumoBacter ACE Detection assay, 122 (58,4%) were positive for S. pneumoniae while only 11 (5.3%) samples were positive with lytA and cpsA primers. Therefore, the commercial multiplex PCR test appears to have low specificity in diagnosing S. pneumoniae.