Streptococcus pneumoniae is one of the most frequent causative agents of community acquired pneumoniae, meningitis, sinusitis, bronchitis and otitis media both in children and adults. Conventional laboratory methods may sometimes fail to identify S.pneumoniae. The aims of this study were i) to compare the conventional methods and molecular methods which detected pneumococcal surface antigen A (psaA) and autolysin (lytA) genes; ii) to determine the serotype distribution of S.pneumoniae isolated from the respiratory samples. Randomly chosen 62 S.pneumoniae strains isolated from respiratory samples of patients with clinically proven pneumococcal pneumonia (age range: 1-79 years) between years 2000-2006, were included in the study. Classical microbiological analysis for the isolates included Gram staining, optochin sensitivity test performed in 5% CO2 and ambient air and bile solubility test. Capsular serotyping was performed by using latex particles sensitized with mono-specific typing sera (Statens Serum Institut, Denmark). Quellung reaction (Statens Serum Institut, Denmark) was used for serotyping the isolates that gave equivocal results using latex agglutination. Pneumococcal surface antigen A and autolysin genes were detected by in-house polymerase chain reaction (PCR) using psaA1 (5′-CTT TCT GCA ATC ATT CTT G), psaA2 (5′-GCC TTC TTT ACC TTG TTC TGC), lytAF (5′-ACG CAA TCT AGC AGA TGA AGC) and lytAR (5′-TGT TTG GTT GGT TAT TCG TGC) primers. Twenty six different serotypes were detected in 62 S.pneumoniae isolates. The most prevalent capsule serotype was 14 (n=6), followed by 19A (n=5). Four isolates could not be typed by the available antisera. All the isolates were optochin sensitive with or without carbondioxide incubation and were bile soluble. All the isolates included in the study have harboured (100%) psaA and lytA genes. No difference was found between the classical and molecular methods for the identification of S.pneumonioe isolates. In conclusion, detection of psaA and/or lytA genes by molecular methods is of value especially in "nonserotypeable strains" when they are performed with conventional methods in clinically proven S.pneumoniae isolates.