The review encompasses a systematic description of the methods available in the clinical setting for diagnostic evaluation of lower respiratory tract infections. Among the tracheo-broncho-alveolar secretions, examination of a representative sputum sample still holds an important role. Introduction of fiberoptic bronchoscopy has improved the diagnostic yield considerably, especially in immunocompromised patients with severe pneumonia. Fiberoptic bronchoscopy in local anaesthesia allows the collection of secretions from the lower respiratory tract through broncho-alveolar lavage (BAL), as well as protected specimen brush and, on certain indications, transbronchial lung biopsy. In severe pneumonia, a specific diagnosis is mandatory in order to design a rational treatment. The diagnosis should be obtained early in the course of the disease, by the use of procedures displaying an appropriate balance between diagnostic yield, incidence of complications and costs. The evaluation of patients with infectious lung disease implies collaboration between pulmonary medicine, infectious medicine, clinical microbiology and pathology.