Linking continuous community-based morbidity recording of influenza-like illness (ILI) with virological sampling has consistently proved its value as one of the earliest indicators of circulating influenza activity. The clinical morbidity recording in the Portuguese national surveillance network, during a 7-year period, and the contribution of different diagnostic techniques, including virus isolation, multiplex RT-PCR, immunocapture enzyme linked immunoassay (EIA) and complement fixation tests (CFTs) for the detection of influenza in such a community-based setting is described and evaluated in this study. There was good correlation between the increase of morbidity, total samples taken and the detection of influenza virus by all the methods although this was less evident for virus isolation and EIA than for RT-PCR or serology. From a total of 1685 throat swabs collected from cases of ILI, 43.6% were RT-PCR positive, 17.5% were positive by capture EIA and in 5% virus isolates were made. The detection of influenza by RT-PCR occurred earlier than by any other method and showed the best correlation with epidemic patterns of morbidity registration. We conclude that in surveillance systems where virus culture is sub-optimal, RT-PCR provides a rapid, sensitive, specific method for detecting influenza viruses from community-based sampling.