Each factor infection or non-infection (surgery, burn) can be the cause of inflammatory reaction development and in turn releasing of pro- and antiinflammatory mediators. Excessive or/and uncontrol releasing of these mediators leads to endothelium damage and organ dysfunction. Standard analysis of common infection markers, i.e. peripheral blood leukocytes, C-reactive protein, reaction of Biernacki measurements, do not allow to distinguish infection and noninfection reason of systemic inflammatory response. Procalcitonin is the specific marker for bacterial and fungal infection. Its level is low during local bacterial and virus infection, autoimmunological diseases, but it is increased at the patients with sepsis, severe sepsis. In described case (patient with Wegener's granulomatosis) applying procalcitonin measurement and sensitive and specific microbiological diagnostic by using bronchio-alveolal lavage leads to successful treatment.