The main aim of the microbiological diagnosis is to detect the etiologic agent of an infection. In case of bacteria it means to check the susceptibility to antibiotics. It can be difficult to find the etiological agent of respiratory tract infections due to wide range of potential pathogens both viral and bacterial. Culture methods are the most frequently used while in case of atypical and viral pathogens rather serological methods based on specific antibody level checking are recommended. In high standard level laboratories molecular biology methods are more widely used. They allow to detect in short time the existence of typical bacteria like Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, atypical ones like Mycoplasma, Chlamydia, and viral pathogens like influenza virus, parainfluenza virus, adenovirus, RSV and rhinovirus. In fact it is very difficult in Poland to get access to high level laboratories for primary care physicians. This is the reason why the treatment of respiratory tract infections is mainly empirical and based on guidelines developed by experts.