Although influenza is recognized for its worldwide importance, little is known about the disease from tropical countries like Indonesia. From August 1999 through January 2003, a surveillance study was conducted in clinics at 6 sentinel locations. Adults (age, >14 years) and children (age, 4-14 years) presenting with respiratory symptoms suggestive of influenza were asked to enroll in the study. Nasal and pharyngeal swabs were examined by virus isolation, polymerase chain reaction, and rapid immunochromatographic tests. A total of 3079 specimens were collected from 1544 participants. Influenza infection was confirmed in 172 volunteers (11.1%) presenting with influenza-like illness. Influenza A (H1N1 and H3N2) and B viruses were detected at all sites. Peak prevalence tended to coincide with the respective rainy seasons, regardless of location. In light of the recent epidemic of severe acute respiratory syndrome, continued influenza surveillance would be useful in strengthening the infrastructure of the Indonesian public health system.