Herpes virus infections represent common complications associated with respiratory tract involvement which may result in pneumonia development in immunocompromised patients. The analysis of bronchoalveolar lavage (BAL) fluid obtained from the lower respiratory tract may contribute to detection of aetiological agents of the disease. The routine use of quantitative molecular methods enables the discrimination between acute infection and viral reactivation with asymptomatic virus shedding. The aim of this review is to evaluate the contribution of BAL viral load monitoring in high-risk patients and to determine the cut-off of viral load leading to progression to herpes virus pneumonia.