A potentially fatal complication of influenza infection is the involvement of the lower respiratory tract caused directly by the influenza virus, and the development of secondary bacterial pneumonia. In these cases, and in patients who are at an increased risk for influenza infection complications, confirmation of etiology by laboratory testing is required in order to guide the initiation and duration of antiviral treatment, and for the implementation of infection control measures and surveillance. Recently, the emergence of novel influenza A strains that carry the risk for more severe disease regardless of age or previous health status, has prompted the development of quick and reliable laboratory tests in an effort to optimize their management and reduce morbidity and mortality. Pneumonia related to the 2009 influenza A pandemic was found in many cases to be rapidly progressive, leading to respiratory failure which in many cases was underestimated by commonly used pneumonia severity scores. Given the limited sensitivity of RIDT and immunofluorescence assays, confirmation of pandemic H1N1 influenza A infection can only be made by rRT-PCR or viral culture. Although annual immunization is the most important preventive measure, NI are the agents of choice for chemoprophylaxis in selected high risk patients, and for treatment. Treatment with NI beyond 48 h of symptoms should be considered only for patients with severe disease.