Background: ILI surveillance in Indonesia has been conducted since 2006, but no data on the bacteria can be detected and caused ILI has been obtained. Method: From March to December 2012, Center for Research on Biomedic and Basic Health Technology's laboratory was receiving throat and nose swab specimens from nine Public Health Centers appointed as the sentinels for ILI surveillance. These specimens were analyzed using multiplex PCR method, which detected six panels of bacteria. Results: 175 specimens taken from ILI patients contained three most frequently found species of bacteria: Streptococcus pneumoniae (n=163), Haemophilus influenzae (n=146) andLegionella pneumophila (41). Conclusion: In ILI patients, there are several bacteria most frequently detected in upper respiratory tract such as Streptococcus pneumoniae, Haemophilus influenzae and Legionella pneumophila. (Health Science Indonesia 2013;2:83-6)