To investigate the burden of influenza-like illness (ILI), patients attending an emergency department during the influenza season were tested for several common respiratory viruses, using PCR-based methods. Influenza A viruses were detected in 25 of 103 recruited patients (24%), rhinoviruses in 15%, and respiratory syncytial virus in only one. The data suggest that triage criteria based on ILI case definitions would not contain the spread of the influenza virus during pandemic alerts and could lead to unnecessary isolation of patients with other infections. Application of broader triage criteria followed by timely molecular diagnosis could be effective in preventing new respiratory agent transmission.