A total of 19,973 clinical specimens obtained from suspected cases of pandemic influenza A virus infection were analyzed by real-time reverse transcription-polymerase chain reaction. Mutations in hemagglutinin (HA) gene and alteration at position 275 in neuraminidase (NA) gene of the randomly selected 29 isolates were detected by sequencing analysis. The virus RNA was detected in 47.3% of the clinical specimens. The pandemic flu cases increased from the 42nd week and peaked in the 46th week of 2009. This intensity continued to the end of the study period. Pandemic flu mainly affected children in the 5-14 year age group, without any gender predominance. The analyzed strains had >98.9% homology with vaccine strains and with each other. More than 37% of the isolates had mutation at position D222E/N on HA gene. There was no isolate harbored mutation at the position H275Y of the NA gene, indicating that the virus isolates currently circulating in Turkey are sensitive to oseltamivir.