The number of iatrogenically induced immunodeficient patients increases concurrently with achievements in the field of medicine. The etiology of fever in such immunodeficient patients is often unknown. We therefore develop modern diagnostic multiplex-PCR and chip-based assays for viral infections in order to improve the clinical care. The underlying immunopathology will also be studied in the respiratory airway mucosa by analysing the constitutional expression of innate immune factors and adaptive immune responses. By early detection of severe viral infections in immunocompromised patients it will be possible to decrease the infection-related morbidity and mortality. A better understanding of the immunopathology at mucosal sites can contribute to new antiviral therapeutic strategies.