Important epidemiological modifications have been registered in respiratory infections, both in immunocompetent and immunocompromised hosts. Pathogens with modified antibiotic susceptibility patterns have emerged, which display an increased antibiotic resistance, such as S. pneumoniae, S. aureus, H. influenzae. This trait has a strong impact on the therapeutic choices, particularly when an empiric antibiotic treatment is selected. The prevalence of bacterial species showing non-susceptibility to the most common prescribed antibiotics (betalactams, macrolides etc.) follows a different geographic distribution. Some pathogens have acquired a new epidemiological role in patients affected with immune deficiencies: among them P. carinii and other bacterial, fungal and viral pathogens. The emergence of new, previously unknown, species, has been registered, both bacteria (C. pneumoniae) and viruses (Metapneumovirus, Hantavirus etc.). Such aspects must be considered in the diagnosis of respiratory infections, which should include diagnostic tests for the identification of such pathogens. Among the new respiratory infections severe acute respiratory syndrome (SARS) has quickly become a health care emergency, so that efforts have been made to identify the aetiological agent as well as the main epidemiological and clinical characteristics of the disease. Avian influenza has raised great interest immediately after the first cases of human infection caused by the avian virus, especially after the outbreaks in Asian countries and in the Netherlands. A crucial step in containing infection is the prevention of the disease; efforts are directed toward this endpoint.